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Conserved domains on  [gi|2020834100|ref|XP_040312317|]
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ADP-ribosylation factor-binding protein GGA3 isoform X3 [Puma yagouaroundi]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VHS_GGA3 cd17008
VHS (Vps27/Hrs/STAM) domain of ADP-ribosylation factor-binding protein GGA3; ADP-ribosylation ...
 6-146 3.24e-111

VHS (Vps27/Hrs/STAM) domain of ADP-ribosylation factor-binding protein GGA3; ADP-ribosylation factor-binding protein GGA3 (Golgi-localized, Gamma-ear-containing, Arf-binding 3) regulates the trafficking and is required for the lysosomal degradation of BACE (beta-site APP-cleaving enzyme), the protease that initiates the production of beta-amyloid, which causes Alzheimer's disease. It also plays a key role in GABA (+) transmission, which is important in the regulation of anxiety-like behaviors. GGA3 is a member of the GGA subfamily, which is comprised of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins involved in membrane trafficking between the Trans-Golgi Network (TGN) and endosomes. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (Gamma-Adaptin Ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the Trans-Golgi Network and the endosomal system.


:

Pssm-ID: 340805 [Multi-domain]  Cd Length: 141  Bit Score: 330.07  E-value: 3.24e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100   6 GESLESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEAVQALTVLEACMKNCGRRFHNEVG 85
Cdd:cd17008     1 GESLESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEALQALTVLEACMKNCGRRFHNEVG 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2020834100  86 KFRFLNELIKVVSPKYLGDRVSEKVKTKVIELLYSWTLALPEETKIKDAYHMLKRQGIVQS 146
Cdd:cd17008    81 KFRFLNELIKVVSPKYLGDRVSEKVKTKVIELLYSWTVALPEEAKIKDAYHMLKRQGIVQS 141
GAT_GGA3 cd14240
canonical GAT domain found in ADP-ribosylation factor-binding protein GGA3; GGA3, also called ...
 213-299 9.16e-56

canonical GAT domain found in ADP-ribosylation factor-binding protein GGA3; GGA3, also called Golgi-localized gamma ear-containing Arf-binding protein 3, belongs to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. GGA3 interacts selectively with the Met/Hepatocyte Growth Factor receptor tyrosine kinase (RTK) when stimulated. It functions as a specific cargo adaptor to target the Met RTK into recycling tubules, and further coordinates the recycling, signaling and degradative fates of the Met RTK. Moreover, GGA3, together with PACS-1 and the protein kinase CK2, forms a complex that regulates cation-independent mannose-6-phosphate receptor (CI-MPR) trafficking. Furthermore, GGA3 has been identified as an interacting protein of the beta-site APP-cleaving enzyme-1 (BACE1), a stress-related protease that is involved in Alzheimer's disease (AD) pathology. GGA3 has a multidomain structure consisting of an N-terminal VHS (Vps27/Hrs/Stam) domain, a GAT (GGA and TOM) domain, a largely unstructured hinge region that contains clathrin-binding motifs, and a C-terminal GAE (gamma-adaptin ear homology) domain. The GAT domain of GGAs interacts with class I GTP-bound form of Arf proteins, Rabaptin-5, ubiquitin, and/or the tumor susceptibility gene 101 product (TSG101).


:

Pssm-ID: 410587  Cd Length: 87  Bit Score: 183.89  E-value: 9.16e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 213 KRLHTLEEVNNNVKLLNEMLLHYSKEDSSEADKELMKELFDRCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVISS 292
Cdd:cd14240     1 KRLHTLEEVNNNVRLLNEMLAHYSKEDSSDGDKELMKELYDRCEKKRRTLFKLASETEDNDNSLGDILQASDDLSRVINS 80


                  ....*..
gi 2020834100 293 YKTVVEG 299
Cdd:cd14240    81 YKKIVEG 87
Alpha_adaptinC2 smart00809
Adaptin C-terminal domain; Adaptins are components of the adaptor complexes which link ...
 521-635 1.44e-31

Adaptin C-terminal domain; Adaptins are components of the adaptor complexes which link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. Gamma-adaptin is a subunit of the golgi adaptor. Alpha adaptin is a heterotetramer that regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This Ig-fold domain is found in alpha, beta and gamma adaptins and consists of a beta-sandwich containing 7 strands in 2 beta-sheets in a greek-key topology.. The adaptor appendage contains an additional N-terminal strand.


:

Pssm-ID: 197886 [Multi-domain]  Cd Length: 104  Bit Score: 118.11  E-value: 1.44e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  521 AYDKNGFRILFHFAKecppgRPDVLVVVVSMLNTAPLPIKSIVLQAAVPKSMKVKLQPPSGTELSPFSPIQppaaitQVM 600
Cdd:smart00809   1 AYEKNGLQIGFKFER-----RPGLIRITLTFTNKSPSPITNFSFQAAVPKSLKLQLQPPSSPTLPPGGQIT------QVL 69

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 2020834100  601 LLANPLKEKARLRYRLTFALGEQLSTEVGEVDQFP 635
Cdd:smart00809  70 KVENPGKFPLRLRLRLSYLLGGSAVTEQGDVLKFP 104
GGA_N-GAT pfam18308
N-terminal extension of GAT domain; This region is found in the N-terminal region of the GGA ...
 169-207 1.32e-09

N-terminal extension of GAT domain; This region is found in the N-terminal region of the GGA and Tom1 (GAT) domain in Golgi-localizing gamma-adaptin ARF-binding protein 1 (GGA1) present in Homo sapiens. The GAT domain is the key region in GGA that interacts with ARF. ARF plays a crucial role in docking adaptor proteins to membranes. This region is referred to as N-GAT and it interacts extensively with ARF.


:

Pssm-ID: 465702  Cd Length: 39  Bit Score: 53.85  E-value: 1.32e-09
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2020834100 169 FDDEEKSKLLAKLLKSKNPDDLQEANKLIKSMVKEDEAR 207
Cdd:pfam18308   1 FDDEEKSKLLARLLKSKNPEDLQAANRLIKSMVKEDDER 39
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 304-594 5.22e-07

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 53.40  E-value: 5.22e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  304 GEVATSAIPDSEGLADPAPTAP---PTESAGNSQWPLFQNEQLDLDFGGP---------EPGSA--AASPSDGP----LV 365
Cdd:PHA03247  2610 GPAPPSPLPPDTHAPDPPPPSPspaANEPDPHPPPTVPPPERPRDDPAPGrvsrprrarRLGRAaqASSPPQRPrrraAR 2689

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  366 PPSAPSAGSSQAPLPPSFPAPAVPASVPA-PKPGSFLFPTGPAPALKAEPTAlgyHGSALGDSTlhqlDALDHLLEETRA 444
Cdd:PHA03247  2690 PTVGSLTSLADPPPPPPTPEPAPHALVSAtPLPPGPAAARQASPALPAAPAP---PAVPAGPAT----PGGPARPARPPT 2762

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  445 TSGLVKPVSSIFFPG----ATTSPLVPTSTTARPLLPFSPGPSSPlfqPQGSPMKGPELSLASVHVPLESiKPSSALPVT 520
Cdd:PHA03247  2763 TAGPPAPAPPAAPAAgpprRLTRPAVASLSESRESLPSPWDPADP---PAAVLAPAAALPPAASPAGPLP-PPTSAQPTA 2838

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  521 AYDKNGFRILF-----------HFAKECPPGRPdvlvvvVSMLNTAPLPIKSIVLQAAVPKSMKVKLQPPSGTELSPFSP 589
Cdd:PHA03247  2839 PPPPPGPPPPSlplggsvapggDVRRRPPSRSP------AAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQ 2912


                   ....*
gi 2020834100  590 IQPPA 594
Cdd:PHA03247  2913 APPPP 2917
 
Name Accession Description Interval E-value
VHS_GGA3 cd17008
VHS (Vps27/Hrs/STAM) domain of ADP-ribosylation factor-binding protein GGA3; ADP-ribosylation ...
 6-146 3.24e-111

VHS (Vps27/Hrs/STAM) domain of ADP-ribosylation factor-binding protein GGA3; ADP-ribosylation factor-binding protein GGA3 (Golgi-localized, Gamma-ear-containing, Arf-binding 3) regulates the trafficking and is required for the lysosomal degradation of BACE (beta-site APP-cleaving enzyme), the protease that initiates the production of beta-amyloid, which causes Alzheimer's disease. It also plays a key role in GABA (+) transmission, which is important in the regulation of anxiety-like behaviors. GGA3 is a member of the GGA subfamily, which is comprised of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins involved in membrane trafficking between the Trans-Golgi Network (TGN) and endosomes. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (Gamma-Adaptin Ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the Trans-Golgi Network and the endosomal system.


Pssm-ID: 340805 [Multi-domain]  Cd Length: 141  Bit Score: 330.07  E-value: 3.24e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100   6 GESLESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEAVQALTVLEACMKNCGRRFHNEVG 85
Cdd:cd17008     1 GESLESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEALQALTVLEACMKNCGRRFHNEVG 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2020834100  86 KFRFLNELIKVVSPKYLGDRVSEKVKTKVIELLYSWTLALPEETKIKDAYHMLKRQGIVQS 146
Cdd:cd17008    81 KFRFLNELIKVVSPKYLGDRVSEKVKTKVIELLYSWTVALPEEAKIKDAYHMLKRQGIVQS 141
VHS pfam00790
VHS domain; Domain present in VPS-27, Hrs and STAM.
 8-142 2.64e-59

VHS domain; Domain present in VPS-27, Hrs and STAM.


Pssm-ID: 395638  Cd Length: 136  Bit Score: 194.83  E-value: 2.64e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100   8 SLESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEAVQALTVLEACMKNCGRRFHNEVGKF 87
Cdd:pfam00790   1 PLERWIDKATDPSLREEDWSLILDICDLINETETGPKEAVRLIKKRINSPNPHVALLALTLLDACVKNCGSKFHLEIASK 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2020834100  88 RFLNELIKVVSPKYLGDRvsEKVKTKVIELLYSWTLAL---PEETKIKDAYHMLKRQG 142
Cdd:pfam00790  81 EFLNELVKLIPNKPYGKP--AKVKKKILELIQEWADAFkndPDLKYIRDMYKLLKRKG 136
GAT_GGA3 cd14240
canonical GAT domain found in ADP-ribosylation factor-binding protein GGA3; GGA3, also called ...
 213-299 9.16e-56

canonical GAT domain found in ADP-ribosylation factor-binding protein GGA3; GGA3, also called Golgi-localized gamma ear-containing Arf-binding protein 3, belongs to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. GGA3 interacts selectively with the Met/Hepatocyte Growth Factor receptor tyrosine kinase (RTK) when stimulated. It functions as a specific cargo adaptor to target the Met RTK into recycling tubules, and further coordinates the recycling, signaling and degradative fates of the Met RTK. Moreover, GGA3, together with PACS-1 and the protein kinase CK2, forms a complex that regulates cation-independent mannose-6-phosphate receptor (CI-MPR) trafficking. Furthermore, GGA3 has been identified as an interacting protein of the beta-site APP-cleaving enzyme-1 (BACE1), a stress-related protease that is involved in Alzheimer's disease (AD) pathology. GGA3 has a multidomain structure consisting of an N-terminal VHS (Vps27/Hrs/Stam) domain, a GAT (GGA and TOM) domain, a largely unstructured hinge region that contains clathrin-binding motifs, and a C-terminal GAE (gamma-adaptin ear homology) domain. The GAT domain of GGAs interacts with class I GTP-bound form of Arf proteins, Rabaptin-5, ubiquitin, and/or the tumor susceptibility gene 101 product (TSG101).


Pssm-ID: 410587  Cd Length: 87  Bit Score: 183.89  E-value: 9.16e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 213 KRLHTLEEVNNNVKLLNEMLLHYSKEDSSEADKELMKELFDRCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVISS 292
Cdd:cd14240     1 KRLHTLEEVNNNVRLLNEMLAHYSKEDSSDGDKELMKELYDRCEKKRRTLFKLASETEDNDNSLGDILQASDDLSRVINS 80


                  ....*..
gi 2020834100 293 YKTVVEG 299
Cdd:cd14240    81 YKKIVEG 87
VHS smart00288
Domain present in VPS-27, Hrs and STAM; Unpublished observations. Domain of unknown function.
 9-142 2.80e-51

Domain present in VPS-27, Hrs and STAM; Unpublished observations. Domain of unknown function.


Pssm-ID: 197630 [Multi-domain]  Cd Length: 133  Bit Score: 173.25  E-value: 2.80e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100    9 LESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEAVQALTVLEACMKNCGRRFHNEVGKFR 88
Cdd:smart00288   1 VERLIDKATSPSLLEEDWELILEICDLINSTPDGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCGSKFHLEVASKE 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2020834100   89 FLNELIKVVSPKYLGdrvsEKVKTKVIELLYSWTLAL---PEETKIKDAYHMLKRQG 142
Cdd:smart00288  81 FLNELVKLIKPKYPL----PLVKKRILELIQEWADAFkndPDLSQIVDVYDLLKKKG 133
Alpha_adaptinC2 smart00809
Adaptin C-terminal domain; Adaptins are components of the adaptor complexes which link ...
 521-635 1.44e-31

Adaptin C-terminal domain; Adaptins are components of the adaptor complexes which link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. Gamma-adaptin is a subunit of the golgi adaptor. Alpha adaptin is a heterotetramer that regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This Ig-fold domain is found in alpha, beta and gamma adaptins and consists of a beta-sandwich containing 7 strands in 2 beta-sheets in a greek-key topology.. The adaptor appendage contains an additional N-terminal strand.


Pssm-ID: 197886 [Multi-domain]  Cd Length: 104  Bit Score: 118.11  E-value: 1.44e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  521 AYDKNGFRILFHFAKecppgRPDVLVVVVSMLNTAPLPIKSIVLQAAVPKSMKVKLQPPSGTELSPFSPIQppaaitQVM 600
Cdd:smart00809   1 AYEKNGLQIGFKFER-----RPGLIRITLTFTNKSPSPITNFSFQAAVPKSLKLQLQPPSSPTLPPGGQIT------QVL 69

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 2020834100  601 LLANPLKEKARLRYRLTFALGEQLSTEVGEVDQFP 635
Cdd:smart00809  70 KVENPGKFPLRLRLRLSYLLGGSAVTEQGDVLKFP 104
Alpha_adaptinC2 pfam02883
Adaptin C-terminal domain; Alpha adaptin is a heterotetramer which regulates clathrin-bud ...
 518-635 6.59e-28

Adaptin C-terminal domain; Alpha adaptin is a heterotetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This ig-fold domain is found in alpha, beta and gamma adaptins.


Pssm-ID: 460735  Cd Length: 111  Bit Score: 108.18  E-value: 6.59e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 518 PVTAYDKNGFRILFHFAKecpPGRPDVLVVVVSMLNTAPLPIKSIVLQAAVPKSMKVKLQPPSGTELSPFspiqPPAAIT 597
Cdd:pfam02883   2 PVVLYESDGLQIGFSFER---SRRPGQIRITLTFTNKSSSPISNFSFQAAVPKSLKLQLQPPSSNVLPPN----PGGQIT 74

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2020834100 598 QVMLLANPLKEKARLRYRLTFaLGEQLSTEVGEVDQFP 635
Cdd:pfam02883  75 QVLLIENPGKKPLRMRLKISY-LNGGAVQEQGDVLKFP 111
GAT pfam03127
GAT domain; The GAT domain is responsible for binding of GGA proteins to several members of ...
 222-299 1.82e-23

GAT domain; The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 and ARF3. The GAT domain stabilizes membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins.


Pssm-ID: 460818  Cd Length: 76  Bit Score: 94.14  E-value: 1.82e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2020834100 222 NNNVKLLNEMLLHYSKEDssEADKELMKELFDRCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVISSYKTVVEG 299
Cdd:pfam03127   1 RNNAKLLNEMLSSTDPDE--ELDNELIKELYERCKSAQPKIQKLIEETSDEDDLLAELLQLNDDLNNVLERYERLKKG 76
GGA_N-GAT pfam18308
N-terminal extension of GAT domain; This region is found in the N-terminal region of the GGA ...
 169-207 1.32e-09

N-terminal extension of GAT domain; This region is found in the N-terminal region of the GGA and Tom1 (GAT) domain in Golgi-localizing gamma-adaptin ARF-binding protein 1 (GGA1) present in Homo sapiens. The GAT domain is the key region in GGA that interacts with ARF. ARF plays a crucial role in docking adaptor proteins to membranes. This region is referred to as N-GAT and it interacts extensively with ARF.


Pssm-ID: 465702  Cd Length: 39  Bit Score: 53.85  E-value: 1.32e-09
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2020834100 169 FDDEEKSKLLAKLLKSKNPDDLQEANKLIKSMVKEDEAR 207
Cdd:pfam18308   1 FDDEEKSKLLARLLKSKNPEDLQAANRLIKSMVKEDDER 39
PHA03247 PHA03247
large tegument protein UL36; Provisional
 304-594 5.22e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 53.40  E-value: 5.22e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  304 GEVATSAIPDSEGLADPAPTAP---PTESAGNSQWPLFQNEQLDLDFGGP---------EPGSA--AASPSDGP----LV 365
Cdd:PHA03247  2610 GPAPPSPLPPDTHAPDPPPPSPspaANEPDPHPPPTVPPPERPRDDPAPGrvsrprrarRLGRAaqASSPPQRPrrraAR 2689

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  366 PPSAPSAGSSQAPLPPSFPAPAVPASVPA-PKPGSFLFPTGPAPALKAEPTAlgyHGSALGDSTlhqlDALDHLLEETRA 444
Cdd:PHA03247  2690 PTVGSLTSLADPPPPPPTPEPAPHALVSAtPLPPGPAAARQASPALPAAPAP---PAVPAGPAT----PGGPARPARPPT 2762

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  445 TSGLVKPVSSIFFPG----ATTSPLVPTSTTARPLLPFSPGPSSPlfqPQGSPMKGPELSLASVHVPLESiKPSSALPVT 520
Cdd:PHA03247  2763 TAGPPAPAPPAAPAAgpprRLTRPAVASLSESRESLPSPWDPADP---PAAVLAPAAALPPAASPAGPLP-PPTSAQPTA 2838

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  521 AYDKNGFRILF-----------HFAKECPPGRPdvlvvvVSMLNTAPLPIKSIVLQAAVPKSMKVKLQPPSGTELSPFSP 589
Cdd:PHA03247  2839 PPPPPGPPPPSlplggsvapggDVRRRPPSRSP------AAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQ 2912


                   ....*
gi 2020834100  590 IQPPA 594
Cdd:PHA03247  2913 APPPP 2917
half-pint TIGR01645
poly-U binding splicing factor, half-pint family; The proteins represented by this model ...
 309-415 3.76e-04

poly-U binding splicing factor, half-pint family; The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.


Pssm-ID: 130706 [Multi-domain]  Cd Length: 612  Bit Score: 43.52  E-value: 3.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 309 SAIPDSEGLADPAPTAPPTES---AGNS------QWPLFQNEQLDLDFGGPEPGSAAASPSDgpLVPPSAPSAGSSQAPL 379
Cdd:TIGR01645 295 SAIPAAAAVAAAAATAKIMAAeavAGAAvlgpraQSPATPSSSLPTDIGNKAVVSSAKKEAE--EVPPLPQAAPAVVKPG 372

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2020834100 380 PPSFPAPAVPASVPAP---KPGSFLFPTGPAPALKAEPT 415
Cdd:TIGR01645 373 PMEIPTPVPPPGLAIPslvAPPGLVAPTEINPSFLASPR 411
COG5373 COG5373
Uncharacterized membrane protein [Function unknown];
350-397 2.86e-03

Uncharacterized membrane protein [Function unknown];


Pssm-ID: 444140 [Multi-domain]  Cd Length: 854  Bit Score: 40.75  E-value: 2.86e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2020834100 350 PEPGSAAASPSDGPLVPPSAPSAGSSQAPLPPSFPAPAVPASVPAPKP 397
Cdd:COG5373    50 PEPEAAAAATAAAPEAAPAPVPEAPAAPPAAAEAPAPAAAAPPAEAEP 97
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 236-604 3.38e-03

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 40.52  E-value: 3.38e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 236 SKEDS-SEADKELMKELFDRCENKRRTLFKLASETEDNDNSlgdilQASDNLSRVISSYKTVVEGQvvnGEVATSAIPDS 314
Cdd:pfam03154  57 SKAESmKKSSKKIKEEAPSPLKSAKRQREKGASDTEEPERA-----TAKKSKTQEISRPNSPSEGE---GESSDGRSVND 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 315 EGLADPAPTAPPTESAGNSqWPLFQNEQLDLDFGGPEPGSAAASPS----DGPLVPPSAPSAGSSQAPLPPsfPAPAVPA 390
Cdd:pfam03154 129 EGSSDPKDIDQDNRSTSPS-IPSPQDNESDSDSSAQQQILQTQPPVlqaqSGAASPPSPPPPGTTQAATAG--PTPSAPS 205

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 391 SVPAPKPGSFLFPTGPAPAlkAEPTALGYHGSALGDSTL-HQLDALDHLLEETRATSGLVKPVSSIFFPGATtsPLVPTS 469
Cdd:pfam03154 206 VPPQGSPATSQPPNQTQST--AAPHTLIQQTPTLHPQRLpSPHPPLQPMTQPPPPSQVSPQPLPQPSLHGQM--PPMPHS 281

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 470 TTARPLLPFSPGPSSPL-FQPQGSPMKGPELSLASVHVPLESIK----PSSALPvtaydkngfrilfhfaKECPPGRPDV 544
Cdd:pfam03154 282 LQTGPSHMQHPVPPQPFpLTPQSSQSQVPPGPSPAAPGQSQQRIhtppSQSQLQ----------------SQQPPREQPL 345

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2020834100 545 LVVVVSMLNTAPLPIKSIVlQAAVPKSMKvklQPPSGTELSPF---SPIQPPAAITQVMLLAN 604
Cdd:pfam03154 346 PPAPLSMPHIKPPPTTPIP-QLPNPQSHK---HPPHLSGPSPFqmnSNLPPPPALKPLSSLST 404
KLF9_13_N-like cd21975
Kruppel-like factor (KLF) 9, KLF13, KLF14, KLF16, and similar proteins; Kruppel/Krueppel-like ...
 298-423 6.96e-03

Kruppel-like factor (KLF) 9, KLF13, KLF14, KLF16, and similar proteins; Kruppel/Krueppel-like transcription factors (KLFs) belong to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. KLF9, KLF10, KLF11, KLF13, KLF14, and KLF16 share a conserved alpha-helical motif AA/VXXL that mediates their binding to Sin3A and their activities as transcriptional repressors. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the related N-terminal domains of KLF9, KLF13, KLF14, KLF16, and similar proteins.


Pssm-ID: 409240 [Multi-domain]  Cd Length: 163  Bit Score: 37.75  E-value: 6.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 298 EGQVVNGEVATSAIPDSEGLADPAPTAPPTESAGNSQWPLFQNEQLDLDfGGPEPGSAAASPSDGPLV-PPSAPSAGSSQ 376
Cdd:cd21975    32 AGLDVRATREVAKGPGPPGPAWKPDGADSPGLVTAAPHLLAANVLAPLR-GPSVEGSSLESGDADMGSdSDVAPASGAAA 110

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2020834100 377 APLP-PSFPAPAVPASVPAPKPG-SFLFPTGPAPALKAEPTALGYHGSA 423
Cdd:cd21975   111 STSPeSSSDAASSPSPLSLLHPGeAGLEPERPRPRVRRGVRRRGVTPAA 159
 
Name Accession Description Interval E-value
VHS_GGA3 cd17008
VHS (Vps27/Hrs/STAM) domain of ADP-ribosylation factor-binding protein GGA3; ADP-ribosylation ...
 6-146 3.24e-111

VHS (Vps27/Hrs/STAM) domain of ADP-ribosylation factor-binding protein GGA3; ADP-ribosylation factor-binding protein GGA3 (Golgi-localized, Gamma-ear-containing, Arf-binding 3) regulates the trafficking and is required for the lysosomal degradation of BACE (beta-site APP-cleaving enzyme), the protease that initiates the production of beta-amyloid, which causes Alzheimer's disease. It also plays a key role in GABA (+) transmission, which is important in the regulation of anxiety-like behaviors. GGA3 is a member of the GGA subfamily, which is comprised of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins involved in membrane trafficking between the Trans-Golgi Network (TGN) and endosomes. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (Gamma-Adaptin Ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the Trans-Golgi Network and the endosomal system.


Pssm-ID: 340805 [Multi-domain]  Cd Length: 141  Bit Score: 330.07  E-value: 3.24e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100   6 GESLESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEAVQALTVLEACMKNCGRRFHNEVG 85
Cdd:cd17008     1 GESLESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEALQALTVLEACMKNCGRRFHNEVG 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2020834100  86 KFRFLNELIKVVSPKYLGDRVSEKVKTKVIELLYSWTLALPEETKIKDAYHMLKRQGIVQS 146
Cdd:cd17008    81 KFRFLNELIKVVSPKYLGDRVSEKVKTKVIELLYSWTVALPEEAKIKDAYHMLKRQGIVQS 141
VHS_GGA_metazoan cd03567
VHS (Vps27/Hrs/STAM) domain of metazoan GGA (Golgi-localized, Gamma-ear-containing, ...
 8-144 8.94e-96

VHS (Vps27/Hrs/STAM) domain of metazoan GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) proteins; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprises a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins involved in membrane trafficking between the Trans-Golgi Network (TGN) and endosomes. Jawed vertebrates contain as many as three GGA proteins: GGA1, GGA2, and GGA3. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (Gamma-Adaptin Ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the Trans-Golgi Network and the endosomal system.


Pssm-ID: 340769  Cd Length: 139  Bit Score: 290.26  E-value: 8.94e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100   8 SLESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEAVQALTVLEACMKNCGRRFHNEVGKF 87
Cdd:cd03567     1 SLEYLLNKATNPFNTEEDWEAIDAFCDRVNKEPEGPQIAVRLLAHKIQSPNEKEALRALTVLEACVKNCGPRFHSEVGKF 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2020834100  88 RFLNELIKVVSPKYLGDRVSEKVKTKVIELLYSWTLALPEETKIKDAYHMLKRQGIV 144
Cdd:cd03567    81 RFLNELIKLVSPKYLGNRTPEEVKQKIIELLYSWTRSLPHEPKIKEAYDMLKKQGII 137
VHS_GGA1 cd17009
VHS (Vps27/Hrs/STAM) domain of ADP-ribosylation factor-binding protein GGA1; ADP-ribosylation ...
 8-146 1.35e-86

VHS (Vps27/Hrs/STAM) domain of ADP-ribosylation factor-binding protein GGA1; ADP-ribosylation factor-binding protein GGA1 (Golgi-localized, Gamma-ear-containing, Arf-binding 1) is also called Gamma-adaptin-related protein 1. It is expressed in human brain and affects the generation of amyloid beta-peptide, and may be involved in the pathogenesis of Alzheimer disease. It is a member of the GGA subfamily, which is comprised of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins involved in membrane trafficking between the Trans-Golgi Network (TGN) and endosomes. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (Gamma-Adaptin Ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the Trans-Golgi Network and the endosomal system.


Pssm-ID: 340806 [Multi-domain]  Cd Length: 139  Bit Score: 266.46  E-value: 1.35e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100   8 SLESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEAVQALTVLEACMKNCGRRFHNEVGKF 87
Cdd:cd17009     1 TLEARINRATNPLNKELDWASINGFCEQLNEEFEGPPLATRLLAHKIQSPQEWEAIQALTVLETCMKSCGKRFHDEVGKF 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2020834100  88 RFLNELIKVVSPKYLGDRVSEKVKTKVIELLYSWTLALPEETKIKDAYHMLKRQGIVQS 146
Cdd:cd17009    81 RFLNELIKVVSPKYLGSRTPEKVKNKILELLYSWTVGLPEEVKIAEAYQMLKKQGIVKS 139
VHS_GGA2 cd17010
VHS (Vps27/Hrs/STAM) domain of ADP-ribosylation factor-binding protein GGA2; ADP-ribosylation ...
 8-145 1.40e-81

VHS (Vps27/Hrs/STAM) domain of ADP-ribosylation factor-binding protein GGA2; ADP-ribosylation factor-binding protein GGA2 (Golgi-localized, Gamma-ear-containing, Arf-binding 2) is also called Gamma-adaptin-related protein 2 and VHS domain and ear domain of gamma-adaptin (Vear). It is a member of the GGA subfamily, which is comprised of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins involved in membrane trafficking between the Trans-Golgi Network (TGN) and endosomes. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (Gamma-Adaptin Ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the Trans-Golgi Network and the endosomal system.


Pssm-ID: 340807  Cd Length: 139  Bit Score: 253.66  E-value: 1.40e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100   8 SLESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEAVQALTVLEACMKNCGRRFHNEVGKF 87
Cdd:cd17010     1 SLESWLNKATDPSNSEEDWECIQGFCEQVNKEPEGPQIATRLLAHKIQSPQEREALHALTVLEMCMNNCGERFHSEVAKF 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2020834100  88 RFLNELIKVVSPKYLGDRVSEKVKTKVIELLYSWTLALPEETKIKDAYHMLKRQGIVQ 145
Cdd:cd17010    81 RFLNELIKVLSPKYLGTWSSEKVKSRVIEVLFSWTVWLPEEVKIRDAYQMLKKQGIIK 138
VHS_GGA cd16977
VHS (Vps27/Hrs/STAM) domain of GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) ...
 9-141 3.10e-81

VHS (Vps27/Hrs/STAM) domain of GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprises a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins involved in membrane trafficking between the Trans-Golgi Network (TGN) and endosomes. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (Gamma-Adaptin Ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the Trans-Golgi Network and the endosomal system.


Pssm-ID: 340774  Cd Length: 133  Bit Score: 252.49  E-value: 3.10e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100   9 LESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEAVQALTVLEACMKNCGRRFHNEVGKFR 88
Cdd:cd16977     1 LERWINRATNPSNAEPDWALILGFCDQINEDGEGPRDAARLLAHKIQSPQEWEAIQALTVLEVCMKNCGYRFHLEVGKFR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2020834100  89 FLNELIKVVSPKYLGDRVSEKVKTKVIELLYSWTLALPEETKIKDAYHMLKRQ 141
Cdd:cd16977    81 FLNELIKVVSPKYLGSRRSEKVKRKILELLYSWTVTLPEEGKIRDAYQMLKKQ 133
VHS pfam00790
VHS domain; Domain present in VPS-27, Hrs and STAM.
 8-142 2.64e-59

VHS domain; Domain present in VPS-27, Hrs and STAM.


Pssm-ID: 395638  Cd Length: 136  Bit Score: 194.83  E-value: 2.64e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100   8 SLESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEAVQALTVLEACMKNCGRRFHNEVGKF 87
Cdd:pfam00790   1 PLERWIDKATDPSLREEDWSLILDICDLINETETGPKEAVRLIKKRINSPNPHVALLALTLLDACVKNCGSKFHLEIASK 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2020834100  88 RFLNELIKVVSPKYLGDRvsEKVKTKVIELLYSWTLAL---PEETKIKDAYHMLKRQG 142
Cdd:pfam00790  81 EFLNELVKLIPNKPYGKP--AKVKKKILELIQEWADAFkndPDLKYIRDMYKLLKRKG 136
GAT_GGA3 cd14240
canonical GAT domain found in ADP-ribosylation factor-binding protein GGA3; GGA3, also called ...
 213-299 9.16e-56

canonical GAT domain found in ADP-ribosylation factor-binding protein GGA3; GGA3, also called Golgi-localized gamma ear-containing Arf-binding protein 3, belongs to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. GGA3 interacts selectively with the Met/Hepatocyte Growth Factor receptor tyrosine kinase (RTK) when stimulated. It functions as a specific cargo adaptor to target the Met RTK into recycling tubules, and further coordinates the recycling, signaling and degradative fates of the Met RTK. Moreover, GGA3, together with PACS-1 and the protein kinase CK2, forms a complex that regulates cation-independent mannose-6-phosphate receptor (CI-MPR) trafficking. Furthermore, GGA3 has been identified as an interacting protein of the beta-site APP-cleaving enzyme-1 (BACE1), a stress-related protease that is involved in Alzheimer's disease (AD) pathology. GGA3 has a multidomain structure consisting of an N-terminal VHS (Vps27/Hrs/Stam) domain, a GAT (GGA and TOM) domain, a largely unstructured hinge region that contains clathrin-binding motifs, and a C-terminal GAE (gamma-adaptin ear homology) domain. The GAT domain of GGAs interacts with class I GTP-bound form of Arf proteins, Rabaptin-5, ubiquitin, and/or the tumor susceptibility gene 101 product (TSG101).


Pssm-ID: 410587  Cd Length: 87  Bit Score: 183.89  E-value: 9.16e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 213 KRLHTLEEVNNNVKLLNEMLLHYSKEDSSEADKELMKELFDRCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVISS 292
Cdd:cd14240     1 KRLHTLEEVNNNVRLLNEMLAHYSKEDSSDGDKELMKELYDRCEKKRRTLFKLASETEDNDNSLGDILQASDDLSRVINS 80


                  ....*..
gi 2020834100 293 YKTVVEG 299
Cdd:cd14240    81 YKKIVEG 87
VHS smart00288
Domain present in VPS-27, Hrs and STAM; Unpublished observations. Domain of unknown function.
 9-142 2.80e-51

Domain present in VPS-27, Hrs and STAM; Unpublished observations. Domain of unknown function.


Pssm-ID: 197630 [Multi-domain]  Cd Length: 133  Bit Score: 173.25  E-value: 2.80e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100    9 LESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEAVQALTVLEACMKNCGRRFHNEVGKFR 88
Cdd:smart00288   1 VERLIDKATSPSLLEEDWELILEICDLINSTPDGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCGSKFHLEVASKE 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2020834100   89 FLNELIKVVSPKYLGdrvsEKVKTKVIELLYSWTLAL---PEETKIKDAYHMLKRQG 142
Cdd:smart00288  81 FLNELVKLIKPKYPL----PLVKKRILELIQEWADAFkndPDLSQIVDVYDLLKKKG 133
VHS_ENTH_ANTH cd00197
VHS, ENTH and ANTH domain superfamily; This superfamily is composed of proteins containing a ...
 9-122 4.93e-47

VHS, ENTH and ANTH domain superfamily; This superfamily is composed of proteins containing a VHS, CID, ENTH, or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The CTD-Interacting Domain (CID) is present in several RNA-processing factors and binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase II (RNAP II or Pol II). The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-Terminal Homology (ANTH) domain. VHS, ENTH, and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH and ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the Trans-Golgi Network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding.


Pssm-ID: 340764  Cd Length: 115  Bit Score: 161.44  E-value: 4.93e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100   9 LESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEAVQALTVLEACMKNCGRRFHNEVGKFR 88
Cdd:cd00197     1 FEKTVEKATSNENMGPDWPLIMEICDLINETNVGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCGERFHQEVASND 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2020834100  89 FLNELIKVVSPKYLGDRVSEKVKTKVIELLYSWT 122
Cdd:cd00197    81 FAVELLKFDKSGLLGDDVSTNVREKAIELVQLWA 114
GAT_GGA_meta cd14234
canonical GAT domain found in metazoan ADP-ribosylation factor (Arf)-binding proteins (GGAs); ...
 213-296 1.95e-40

canonical GAT domain found in metazoan ADP-ribosylation factor (Arf)-binding proteins (GGAs); GGAs, also called Golgi-localized gamma-ear-containing Arf-binding proteins, belong to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. Moreover, GGAs play important roles in ubiquitin-dependent sorting of cargo proteins both in biosynthetic and endocytic pathways. Three GGAs (GGA1, GGA2, and GGA3) have been identified in mammals. They may appear to behave similarly, since all of them have a multidomain structure consisting of: an N-terminal VHS (Vps27/Hrs/Stam) domain that binds the acidic-cluster dileucine (DxxLL)-type sorting signals (where x is any amino acid) found in the cytoplasmic tail of TGN sorting receptors; a GAT (GGA and TOM) domain that interacts with class I GTP-bound form of Arf proteins, Rabaptin-5, ubiquitin, and the tumor susceptibility gene 101 product (TSG101); a largely unstructured hinge region that contains clathrin-binding motifs; and a C-terminal GAE (gamma-adaptin ear homology) domain that binds accessory proteins. However, the three GGAs have some differences, which suggest they may possess their own distinct roles. For instance, both GGA1 and GGA3, but not GGA2, contains an internal DxxLL motif that binds to it own VHS domain. Only a portion of the VHS domain of GGA2 possesses distant structural homology to that of GGA1 or GGA3. Moreover, the binding affinity of GGA2 to ubiquitin is quite lower than that of GGA1 or GGA3. In addition, GGA3 has a short splicing variant that is predominantly expressed in human cell lines and tissues except the brain. It does have a VHS domain, but it is unable to bind to the DxxLL motif. GGA2 and GGA3 undergo epidermal growth factor (EGF)-induced phosphorylation.


Pssm-ID: 410582  Cd Length: 84  Bit Score: 141.98  E-value: 1.95e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 213 KRLHTLEEVNNNVKLLNEMLLHYSKEDSSEADKELMKELFDRCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVISS 292
Cdd:cd14234     1 KRLLELEEVNNNVKLLNEMLDHYSPGESSQDELELMKELYESCEKMRPTLFRLASETDDDDEGLADILQANDELTRVMQR 80


                  ....
gi 2020834100 293 YKTV 296
Cdd:cd14234    81 YKNL 84
GAT_GGA1_GGA2 cd14239
canonical GAT domain found in ADP-ribosylation factor (Arf)-binding proteins GGA1 and GGA2; ...
 210-297 9.90e-40

canonical GAT domain found in ADP-ribosylation factor (Arf)-binding proteins GGA1 and GGA2; This subfamily includes GGA1 and GGA2, both of which belong to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. GGA1, also called gamma-adaptin-related protein 1, or Golgi-localized gamma ear-containing Arf-binding protein 1, regulates the low-density lipoprotein and sorting receptor LR11/SorLA endocytic traffic and further alters amyloid-beta precursor protein (APP) intracellular distribution and amyloid-beta production. It is also critical for the effects of beta-site APP-cleaving enzyme-1 (BACE1) on amyloid-beta generation. It interacts with BACE1 and promotes its traffic from early endosomes to late endocytic compartments or the TGN. Moreover, GGA1 acts as a clathrin assembly protein with the ability to polymerize clathrin into tubules. GGA2, also called gamma-adaptin-related protein 2, Golgi-localized gamma ear-containing Arf-binding protein 2, or VHS domain and ear domain of gamma-adaptin (Vear), interacts with the acidic cluster-dileucine motif in the cytoplasmic tail of the cation-independent mannose 6-phosphate receptor (CI-MPR) and further plays a major role in the sorting of lysosomal enzymes. It also mediates a vital function that cannot be compensated for by GGA1 and/or GGA3. Both GGA1 and GGA2 have a multidomain structure consisting of an N-terminal VHS (Vps27/Hrs/Stam) domain, a GAT (GGA and TOM) domain, a largely unstructured hinge region that contains clathrin-binding motifs, and a C-terminal GAE (gamma-adaptin ear homology) domain. The GAT domain of GGAs interacts with class I GTP-bound form of Arf proteins, Rabaptin-5, ubiquitin, and/or the tumor susceptibility gene 101 product (TSG101).


Pssm-ID: 410586  Cd Length: 88  Bit Score: 140.19  E-value: 9.90e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 210 KVTKRLHTLEEVNNNVKLLNEMLLHYSKEDSSEADKELMKELFDRCENKRRTLFKLASETEDNDNSLGDILQASDNLSRV 289
Cdd:cd14239     1 KVSKRVNAIEEVNNNVKLLTEMLMSYSRGELSESSEELMKELYQRCEKMRPTLFRLASDTEDNDEALAEILQANDNLTQV 80


                  ....*...
gi 2020834100 290 ISSYKTVV 297
Cdd:cd14239    81 INLYKQLV 88
VHS cd03561
VHS (Vps27/Hrs/STAM) domain family; The VHS domain is present in Vps27 (Vacuolar Protein ...
 9-140 1.60e-37

VHS (Vps27/Hrs/STAM) domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family, which has the domain composition of VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition of VHS-GAT (GGA and TOM)-GAE (Gamma-Adaptin Ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general membrane targeting/cargo recognition role in vesicular trafficking.


Pssm-ID: 340765  Cd Length: 131  Bit Score: 135.86  E-value: 1.60e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100   9 LESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEAVQALTVLEACMKNCGRRFHNEVGKFR 88
Cdd:cd03561     1 VEELVEKATSESLTEPDWALNLEICDLVNSDPAQAKDAVRALRKRLQSKNPKVQLLALTLLETLVKNCGAPFHSEVASRD 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2020834100  89 FLNELIKVVSPKylgdRVSEKVKTKVIELLYSWTLALPEETK---IKDAYHMLKR 140
Cdd:cd03561    81 FLQELVKLVKKK----KTSPEVREKALALIQEWAEAFQGDGRlplFYDTYQQLRR 131
GAT_GGA cd14230
canonical GAT domain found in metazoan and fungal ADP-ribosylation factor (Arf)-binding ...
 217-296 2.19e-33

canonical GAT domain found in metazoan and fungal ADP-ribosylation factor (Arf)-binding proteins (GGAs); GGAs, also called Golgi-localized gamma-ear-containing Arf-binding proteins, belong to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. GGAs also play important roles in ubiquitin-dependent sorting of cargo proteins both in biosynthetic and endocytic pathways. The family includes three GGAs (GGA1, GGA2, and GGA3) identified in mammals and two GGAs (Gga1p and Gga2p) identified in the budding yeast Saccharomyces cerevisiae. All these GGAs have a multidomain structure consisting of: an N-terminal VHS (Vps27/Hrs/Stam) domain that binds acidic-cluster dileucine (DxxLL)-type sorting signals (where x is any amino acid) found in the cytoplasmic tail of TGN sorting receptors; a GAT (GGA and TOM) domain that interacts with class I GTP-bound form of Arf proteins, Rabaptin-5, ubiquitin, and the tumor susceptibility gene 101 product (TSG101); a largely unstructured hinge region that contains clathrin-binding motifs; and a C-terminal GAE (gamma-adaptin ear homology) domain that binds accessory proteins. In contrast to other GGAs-like proteins, members of this family contain a GAT N-terminal region, a helix-loop-helix in the complex with Arf1-GTP.


Pssm-ID: 410578  Cd Length: 80  Bit Score: 122.66  E-value: 2.19e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 217 TLEEVNNNVKLLNEMLLHYSKEDSSEADKELMKELFDRCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVISSYKTV 296
Cdd:cd14230     1 TLEEAKNNVDLLDEMLLSYSQEDSSDGDNELMKELYDQLENMRPTLFKLASETEENDNSLGDVLQASDNVNRVINKYKDI 80
Alpha_adaptinC2 smart00809
Adaptin C-terminal domain; Adaptins are components of the adaptor complexes which link ...
 521-635 1.44e-31

Adaptin C-terminal domain; Adaptins are components of the adaptor complexes which link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. Gamma-adaptin is a subunit of the golgi adaptor. Alpha adaptin is a heterotetramer that regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This Ig-fold domain is found in alpha, beta and gamma adaptins and consists of a beta-sandwich containing 7 strands in 2 beta-sheets in a greek-key topology.. The adaptor appendage contains an additional N-terminal strand.


Pssm-ID: 197886 [Multi-domain]  Cd Length: 104  Bit Score: 118.11  E-value: 1.44e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  521 AYDKNGFRILFHFAKecppgRPDVLVVVVSMLNTAPLPIKSIVLQAAVPKSMKVKLQPPSGTELSPFSPIQppaaitQVM 600
Cdd:smart00809   1 AYEKNGLQIGFKFER-----RPGLIRITLTFTNKSPSPITNFSFQAAVPKSLKLQLQPPSSPTLPPGGQIT------QVL 69

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 2020834100  601 LLANPLKEKARLRYRLTFALGEQLSTEVGEVDQFP 635
Cdd:smart00809  70 KVENPGKFPLRLRLRLSYLLGGSAVTEQGDVLKFP 104
Alpha_adaptinC2 pfam02883
Adaptin C-terminal domain; Alpha adaptin is a heterotetramer which regulates clathrin-bud ...
 518-635 6.59e-28

Adaptin C-terminal domain; Alpha adaptin is a heterotetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This ig-fold domain is found in alpha, beta and gamma adaptins.


Pssm-ID: 460735  Cd Length: 111  Bit Score: 108.18  E-value: 6.59e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 518 PVTAYDKNGFRILFHFAKecpPGRPDVLVVVVSMLNTAPLPIKSIVLQAAVPKSMKVKLQPPSGTELSPFspiqPPAAIT 597
Cdd:pfam02883   2 PVVLYESDGLQIGFSFER---SRRPGQIRITLTFTNKSSSPISNFSFQAAVPKSLKLQLQPPSSNVLPPN----PGGQIT 74

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2020834100 598 QVMLLANPLKEKARLRYRLTFaLGEQLSTEVGEVDQFP 635
Cdd:pfam02883  75 QVLLIENPGKKPLRMRLKISY-LNGGAVQEQGDVLKFP 111
VHS_Tom1_like cd03565
VHS (Vps27/Hrs/STAM) domain of Tom1 subfamily; This subfamily is composed of Tom1 (Target of ...
 15-142 8.40e-27

VHS (Vps27/Hrs/STAM) domain of Tom1 subfamily; This subfamily is composed of Tom1 (Target of myb1 - retroviral oncogene) protein, Tom1L1 (Tom1-like1), Tom1L2 (Tom1-like2), and similar proteins. Proteins belonging to this subfamily are characterized by the presence of a VHS (Vps27p/Hrs/Stam) domain in the N-terminal portion followed by a GAT (GGA and Tom) domain. They are novel regulators for post-Golgi trafficking and signaling. Yeast do not contain homologous proteins of the Tom1 subfamily, suggesting these proteins have evolved to accommodate more complex cellular processes. Tom1 is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting.


Pssm-ID: 340768  Cd Length: 138  Bit Score: 105.81  E-value: 8.40e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  15 KATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQ---EWEAVQALTVLEACMKNCGRRFHNEVGKFRFLN 91
Cdd:cd03565     8 RATDSGLSSEDWALNMEICDMINETDDGPKDAIKAIKKRLSTNAgknHTVVMYTLTLLETCVKNCGHRFHVLVANKDFLQ 87

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2020834100  92 ELIKVVSPKYlgdRVSEKVKTKVIELLYSWTLAL---PEETKIKDAYHMLKRQG 142
Cdd:cd03565    88 ELVKLIGPKN---DPPTIVQEKVLSLIQSWADAFrgqPDLQEVVKVYQELKAKG 138
GAT_SF cd12930
GAT domain found in eukaryotic GGAs, metazoan Tom1-like proteins, metazoan STAMs, fungal Vps27, ...
 219-296 1.50e-25

GAT domain found in eukaryotic GGAs, metazoan Tom1-like proteins, metazoan STAMs, fungal Vps27, and similar proteins; The GAT (GGA and Tom1) domain superfamily includes the canonical GAT domain found in ADP-ribosylation factor (Arf)-binding proteins (GGAs) from eukaryotes, myb protein 1 (Tom1)-like proteins from metazoa, and LAS seventeen-binding protein 5 (Lsb5p)-like proteins from fungi. The canonical GAT domain is a monomeric three-helix bundle that binds ubiquitin. GGAs, also called Golgi-localized gamma-ear-containing Arf-binding proteins, belong to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. GGAs play important roles in ubiquitin-dependent sorting of cargo proteins both in biosynthetic and endocytic pathways. Tom1 and its related proteins, Tom1L1 and Tom1L2, form a protein family sharing an N-terminal VHS-domain followed by a GAT domain. Tom1 family proteins bind to ubiquitin, ubiquitinated proteins, and Toll-interacting protein (Tollip) through its GAT domain. They do not associate with either Arf GTPases through its GAT domain nor with acidic cluster-dileucine sequences through its VHS domain. The GAT domain superfamily also includes the non-canonical GAT domain found in several components of the ESCRT-0 complex, including signal transducing adapter molecules (STAMs) and hepatocyte growth factor-regulated tyrosine kinase substrate (Hrs) from metazoa, as well as vacuolar protein sorting-associated protein 27 (Vps27) and class E vacuolar protein-sorting machinery protein Hse1 from fungi. Hrs, together with STAM, forms a Hrs/STAM core complex. Vps27, together with Hse1, forms a Vps27/Hse1 core complex. Those complexes consist of two intertwined GAT domains, each consisting of two helices from one subunit, and one from the other subunit. The intertwined GAT heterodimer acts as a scaffold for binding of ubiquitinated cargo proteins and coordinating ubiquitination and deubiquitination reactions that regulate sorting.


Pssm-ID: 410577  Cd Length: 77  Bit Score: 100.39  E-value: 1.50e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2020834100 219 EEVNNNVKLLNEMLLHYSKEDSSEADKELMKELFDRCENKRRTLFKLASETEdNDNSLGDILQASDNLSRVISSYKTV 296
Cdd:cd12930     1 EEVKDNVR*FSELLEK*KSRPLEILDDELLQELAQRCFASKARLNYLLNDKA-DDQKYNTLLE*NDNLSEV*NIYDRL 77
VHS_Hrs cd03569
VHS (Vps27/Hrs/STAM) domain of Hepatocyte growth factor-regulated tyrosine kinase substrate, ...
 13-142 3.69e-24

VHS (Vps27/Hrs/STAM) domain of Hepatocyte growth factor-regulated tyrosine kinase substrate, Hrs; Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) plays a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane. Together with STAM or STAM2, it comprises the ESCRT (Endosomal Sorting Complex Required for Transport)-0 machinery, which functions to bind and sequester cargoes for downstream sorting into intralumenal vesicles. Hrs contains an N-terminal VHS domain, which has a superhelical structure similar to the structure of ARM (Armadillo) repeats, a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain, a Double Ubiquitin-Interacting Motif (DUIM), a P(S/T)XP motif that recruit ESCRT-I, a GAT (GGA and TOM) domain, and a short peptide motif near the C-terminus that recruits clathrin.


Pssm-ID: 340771  Cd Length: 138  Bit Score: 98.48  E-value: 3.69e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  13 LNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEAVQALTVLEACMKNCGRRFHNEVGKFRFLNE 92
Cdd:cd03569     7 LDKATSQLLLEPDWESILQICDLIRQGDVTPKYAVSAIKKKLNDQNPHVALYALQVLESVVKNCGTPVHDEVATKEFMEE 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2020834100  93 LIKVVSpkylgDRVSEKVKTKVIELLYSWTLALPEETK---IKDAYHMLKRQG 142
Cdd:cd03569    87 LRDLVK-----TTTSENVRNKILELIQAWAHAFRNEPKykiVQDTYNIMKMEG 134
GAT pfam03127
GAT domain; The GAT domain is responsible for binding of GGA proteins to several members of ...
 222-299 1.82e-23

GAT domain; The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 and ARF3. The GAT domain stabilizes membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins.


Pssm-ID: 460818  Cd Length: 76  Bit Score: 94.14  E-value: 1.82e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2020834100 222 NNNVKLLNEMLLHYSKEDssEADKELMKELFDRCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVISSYKTVVEG 299
Cdd:pfam03127   1 RNNAKLLNEMLSSTDPDE--ELDNELIKELYERCKSAQPKIQKLIEETSDEDDLLAELLQLNDDLNNVLERYERLKKG 76
VHS_STAM cd03568
VHS (Vps27/Hrs/STAM) domain of the STAM (Signal Transducing Adaptor Molecule) subfamily; STAM ...
 15-142 4.09e-22

VHS (Vps27/Hrs/STAM) domain of the STAM (Signal Transducing Adaptor Molecule) subfamily; STAM (Signal Transducing Adaptor Molecule) subfamily members have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a Ubiquitin-Interacting Motif (UIM) and a SH3 (Src Homology 3) domain, which is a well-established protein-protein interaction domain, and a GAT (GGA and TOM) domain. At the C-termini of most vertebrate STAMs, an Immunoreceptor Tyrosine-based Activation Motif (ITAM) is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries. STAM is a component of the ESCRT (Endosomal Sorting Complex Required for Transport)-0 machinery and together with Hrs, functions to bind and sequester cargoes for downstream sorting into intralumenal vesicles. Jawed vertebrates have two STAM subfamily members, STAM1 and STAM2.


Pssm-ID: 340770  Cd Length: 132  Bit Score: 92.36  E-value: 4.09e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  15 KATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEAVQALTVLEACMKNCGRRFHNEVGKFRFLNELI 94
Cdd:cd03568     7 KATSEKNTSENWSLILDICDKVGRSPNGAKDCLKSIMKRLNHKDPHVALQALTLLDACVKNCGKIFHLEVCSRDFESELR 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2020834100  95 KVVSpkylgdRVSEKVKTKVIELLYSWTlalpEETKIKDA--------YHMLKRQG 142
Cdd:cd03568    87 KLLT------KSHPKVAEKLKELLKKWA----EEEFKDDPqlslipslYKKLKAEG 132
VHS_Tom1L2 cd16996
VHS (Vps27/Hrs/STAM) domain of TOM1-like protein 2; TOM1-like protein 2 (Tom1L2) is a member ...
 13-142 6.71e-22

VHS (Vps27/Hrs/STAM) domain of TOM1-like protein 2; TOM1-like protein 2 (Tom1L2) is a member of the Tom1 (Target of myb1) subfamily, characterized by the presence of a VHS (Vps27p/Hrs/Stam) domain in the N-terminal portion followed by a GAT (GGA and Tom) domain. They are novel regulators for post-Golgi trafficking and signaling. Studies in Tom1L2 hypomorphic mice suggest that Tom1L2 may play roles in immune responses and tumor suppression. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting.


Pssm-ID: 340793 [Multi-domain]  Cd Length: 137  Bit Score: 92.02  E-value: 6.71e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  13 LNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEW-EAVQALTVLEACMKNCGRRFHNEVGKFRFLN 91
Cdd:cd16996     6 IEKATDGSLQSEDWTLNMEICDIINETEEGPKDAIRALKKRLNGNKNYrEVMLALTVLETCVKNCGHRFHVLVASRDFID 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2020834100  92 E-LIKVVSPKylgDRVSEKVKTKVIELLYSWTLAL---PEETKIKDAYHMLKRQG 142
Cdd:cd16996    86 GvLVKIISPK---NNPPTIVQDKVLALIQAWADAFrssPDLTGVVHIYEELKRKG 137
VHS_HSE1 cd16978
VHS (Vps27/Hrs/STAM) domain of Class E vacuolar protein-sorting machinery protein HSE1; Class ...
 9-142 2.06e-21

VHS (Vps27/Hrs/STAM) domain of Class E vacuolar protein-sorting machinery protein HSE1; Class E vacuolar protein-sorting machinery protein HSE1, together with Vps27, comprise the ESCRT-0 complex, the sorting receptor for ubiquitinated cargo proteins at the multivesicular body (MVB). The complex directly binds to ubiquitinated transmembrane proteins and recruits both ubiquitin ligases and deubiquitinating enzymes. It is also required the efficient recycling of late Golgi proteins including the carboxypeptidase Y (CPY) sorting receptor, Vps10. Similar to metazoan STAMs, HSE1 contain: an N-terminal VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats; a Ubiquitin-Interacting Motif (UIM); a SH3 (Src Homology 3) domain, a well-established protein-protein interaction domain; and a GAT (GGA and TOM) domain, which is essential for the normal sorting function of HSE1.


Pssm-ID: 340775  Cd Length: 134  Bit Score: 90.32  E-value: 2.06e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100   9 LESWLNKATNPSNRQEDWEYIIGFCDQINKELE-GPQIAVRLLAHKIQSPQewEAVQ--ALTVLEACMKNCGRRFHNEVG 85
Cdd:cd16978     1 IDELIIKATDETLTSENWQYILDVCDKVNSDPEdGAREAIAAIQKRLQHRN--ANVQlrSLSLADALAKNCGSRLHQEIS 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  86 KFRFLNELIKVVspkyLGDRVSEKVKTKVIELLYSWTLAL---PEETKIKDAYHMLKRQG 142
Cdd:cd16978    79 SRSFTQTLLRLI----NDRTTHATVKKRILELIKQLSDSFksdPSLGLMSDTYDQLKSKY 134
VHS_Tom1 cd16995
VHS (Vps27/Hrs/STAM) domain of Target of Myb protein 1; Tom1 (Target of myb1 - retroviral ...
 13-142 5.52e-20

VHS (Vps27/Hrs/STAM) domain of Target of Myb protein 1; Tom1 (Target of myb1 - retroviral oncogene) is a novel negative regulator of interleukin-1 and tumor necrosis factor-induced signaling pathways. It also plays important roles in protein-degradation systems in Alzheimer's disease pathogenesis. Tom1 contains VHS and GAT domains in the N-terminal and central region, respectively. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of Tom1 is essential for its function as a negative regulator.


Pssm-ID: 340792  Cd Length: 137  Bit Score: 86.50  E-value: 5.52e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  13 LNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEW-EAVQALTVLEACMKNCGRRFHNEVGKFRFL- 90
Cdd:cd16995     6 IEKATDGSLQSEDWGLNMEICDIINETEEGPKDAIRAIKKRIVGNKNFrEVMLALTVLETCVKNCGHRFHVLVASQDFVe 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2020834100  91 NELIKVVSPKylgDRVSEKVKTKVIELLYSWTLAL---PEETKIKDAYHMLKRQG 142
Cdd:cd16995    86 GVLVKTILPK---NNPPAIVHDKVLNLIQAWADAFrssPDLTGVVTVYEDLRRKG 137
VHS_STAM2 cd16999
VHS (Vps27/Hrs/STAM) domain of Signal Transducing Adapter Molecule 2; Signal Transducing ...
 15-144 1.58e-17

VHS (Vps27/Hrs/STAM) domain of Signal Transducing Adapter Molecule 2; Signal Transducing Adapter Molecule 2 (STAM2) is also called EAST (EGFR-Associated protein with SH3 and TAM domain) and Hbp (Hrs-binding protein). It is highly expressed in neurons, where it is localized in the nucleus. STAM (Signal Transducing Adaptor Molecule) subfamily members have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a Ubiquitin-Interacting Motif (UIM) and a SH3 (Src Homology 3) domain, which is a well-established protein-protein interaction domain, and a GAT (GGA and TOM) domain. At the C-termini of most vertebrate STAMS, an Immunoreceptor Tyrosine-based Activation Motif (ITAM) is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries. STAM is a component of the ESCRT (Endosomal Sorting Complex Required for Transport)-0 machinery and together with Hrs, functions to bind and sequester cargoes for downstream sorting into intralumenal vesicles.


Pssm-ID: 340796 [Multi-domain]  Cd Length: 139  Bit Score: 79.63  E-value: 1.58e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  15 KATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEAVQALTVLEACMKNCGRRFHNEVGKFRFLNELI 94
Cdd:cd16999     7 KATNEYNTSEDWSLIMDICDKVGSTPNGAKDCLKAIMKRVNHKVPHVALQALTLLGACVSNCGKIFHLEVCSRDFATEVR 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2020834100  95 KVVSPKYLGdRVSEKVKTKVIEllysWTLAL---PEETKIKDAYHMLKRQGIV 144
Cdd:cd16999    87 AVIKNKAHP-KVCEKLKALMVE----WSEEFqkdPQFSLISATIKSLKEEGIT 134
VHS_STAM1 cd17000
VHS (Vps27/Hrs/STAM) domain of Signal Transducing Adapter Molecule 1; Signal Transducing ...
 13-142 2.53e-14

VHS (Vps27/Hrs/STAM) domain of Signal Transducing Adapter Molecule 1; Signal Transducing Adapter Molecule 1 (STAM1) is part of a crucial regulatory axis for the ventral axonal trajectory of developing spinal motor neurons. It forms a complex with beta-arrestin, which regulates lysosomal trafficking of the chemokine receptor CXCR4 and also mediates CXCR4-dependent chemotaxis. STAM (Signal Transducing Adaptor Molecule) subfamily members have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a Ubiquitin-Interacting Motif (UIM) and a SH3 (Src Homology 3) domain, which is a well-established protein-protein interaction domain, and a GAT (GGA and TOM) domain. At the C-termini of most vertebrate STAMS, an Immunoreceptor Tyrosine-based Activation Motif (ITAM) is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries. STAM is a component of the ESCRT (Endosomal Sorting Complex Required for Transport)-0 machinery and together with Hrs, functions to bind and sequester cargoes for downstream sorting into intralumenal vesicles.


Pssm-ID: 340797  Cd Length: 131  Bit Score: 70.10  E-value: 2.53e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  13 LNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEAVQALTVLEACMKNCGRRFHNEVGKFRFLNE 92
Cdd:cd17000     5 VEKATSEMNTAEDWGLILDICDKVGQSRTGPKDCLRSIMRRVNHKDPHVAMQALTLLGACVSNCGKIFHLEVCSRDFASE 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2020834100  93 LIKVVSPKYlgDRVSEKVKTKVIEllysWTLAL---PEETKIKDAYHMLKRQG 142
Cdd:cd17000    85 VSNVLNKGH--PKVCEKLKALMVE----WTEEFkndPQLSLISAMIKNLKEQG 131
GAT_GGA_Tom1-like cd21383
canonical GAT domain found in eukaryotic ADP-ribosylation factor (Arf)-binding proteins (GGAs), ...
 218-295 2.67e-14

canonical GAT domain found in eukaryotic ADP-ribosylation factor (Arf)-binding proteins (GGAs), metazoan myb protein 1 (Tom1)-like proteins, and similar proteins; This model represents the canonical GAT (GGA and Tom1) domain found in GGAs from eukaryotes, Tom1-like proteins from metazoa, and LAS seventeen-binding protein 5 (Lsb5p)-like proteins from fungi. The canonical GAT domain is a monomeric three-helix bundle that binds ubiquitin. GGAs, also called Golgi-localized gamma-ear-containing Arf-binding proteins, belong to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. GGAs play important roles in ubiquitin-dependent sorting of cargo proteins both in biosynthetic and endocytic pathways. Tom1 and its related proteins, Tom1L1 and Tom1L2, form a protein family sharing an N-terminal VHS-domain followed by a GAT domain. Tom1 family proteins bind to ubiquitin, ubiquitinated proteins, and Toll-interacting protein (Tollip) through its GAT domain. They do not associate with either Arf GTPases through its GAT domain nor with acidic cluster-dileucine sequences through its VHS domain. In addition, Tom1 family proteins recruit clathrin onto endosomes through their C-terminal region. The C-terminal clathrin-binding region of Tom1 and Tom1L2 are similar to each other, but distinguishable from Tom1L1.


Pssm-ID: 410588  Cd Length: 80  Bit Score: 68.44  E-value: 2.67e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 218 LEEVNNNVKLLNEMLLHYSkeDSSEADKELMKELFDRCENKRRTLFKLASETED--NDNSLGDILQASDNLSRVISSYKT 295
Cdd:cd21383     2 LEEVKENASLLNEMLSAAS--PEELLDNELLQELVEFCRACQPRIVELIEATTDglDEDTLEELLELNDELNEALQRYDD 79
VHS_Tom1L1 cd16997
VHS (Vps27/Hrs/STAM) domain of TOM1-like protein 1; TOM1-like protein 1 (Tom1L1) is also ...
 8-142 5.35e-14

VHS (Vps27/Hrs/STAM) domain of TOM1-like protein 1; TOM1-like protein 1 (Tom1L1) is also called Src-activating and signaling molecule protein (Srcasm). It is a member of the Tom1 (Target of myb1) subfamily, characterized by the presence of a VHS (Vps27p/Hrs/Stam) domain in the N-terminal portion followed by a GAT (GGA and Tom) domain. They are novel regulators for post-Golgi trafficking and signaling. Tom1L1 has been implicated in multivesicular body (MVB) formation, viral egress from the cell, and cytokinesis. Its amplification enhances the metastatic progression of ERBB2-positive breast cancers. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting.


Pssm-ID: 340794  Cd Length: 137  Bit Score: 69.48  E-value: 5.35e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100   8 SLESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEAVQ-ALTVLEACMKNCGRRFHNEVGK 86
Cdd:cd16997     1 SVGHLIEKATFGTVQTEDWGQFMHICDIINTTEDGPKDAVKALKKRISKNYNHKEIRlTLSLLDMCMQNCGPSFQSLVVK 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  87 FRFLNE-LIKVVSPKYlgdRVSEKVKTKVIELLYSWTLALP---EETKIKDAYHMLKRQG 142
Cdd:cd16997    81 KEFVKDvLVKLLNPRY---NLPVDLQNKILNFIMTWAQGFQggvDVSEVKEVYLDLVKKG 137
VHS_Lsb5 cd16980
VHS (Vps27/Hrs/STAM) domain of LAS seventeen-binding protein 5; LAS seventeen-binding protein ...
 11-140 6.43e-14

VHS (Vps27/Hrs/STAM) domain of LAS seventeen-binding protein 5; LAS seventeen-binding protein 5 (LAS17-binding protein 5, Lsb5, or Lsb5p) localizes to the plasma membrane and plays a role in endocytosis in yeast. It interacts with actin regulators Sla1p and Las17p, ubiquitin, and Arf3p, coupling actin dynamics to membrane trafficking processes. Lsb5p contains an N-terminal VHS domain and a GAT (GGA and TOM) domain. The VHS domain has a superhelical structure similar to the structure of ARM (Armadillo) repeats. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting.


Pssm-ID: 340777  Cd Length: 132  Bit Score: 68.78  E-value: 6.43e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  11 SWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQ--SPQEweAVQALTVLEACMKNCGRRFHNEVGKFR 88
Cdd:cd16980     3 DTIERLTSSEYEEEDWSLVLELCELINLIESGAKEAARALRKKLKygNPHQ--QLRALTLLDLLVENGGKKFQAQFASDK 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2020834100  89 FLNELIKVVSPKylgDRVSEKVKTKVIELLYSWTLALPEETK---IKDAYHMLKR 140
Cdd:cd16980    81 KLEDLLRLIASD---PSTDPKVRKKLLELLGGWAYEFKGDPGlsgIASLYKKVKP 132
VHS_GGA_fungi cd16998
VHS (Vps27/Hrs/STAM) domain of fungal GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) ...
 9-133 5.42e-13

VHS (Vps27/Hrs/STAM) domain of fungal GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) proteins; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprises a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins involved in membrane trafficking between the Trans-Golgi Network (TGN) and endosomes. Yeast GGAs facilitate the specific and direct delivery of vacuolar sorting receptor Vps10p and the processing protease Kex2p from the TGN to the late endosome/prevacuolar compartment (PVC). The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (Gamma-Adaptin Ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the Trans-Golgi Network and the endosomal system.


Pssm-ID: 340795 [Multi-domain]  Cd Length: 139  Bit Score: 66.58  E-value: 5.42e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100   9 LESWLNKATNPSNRQEDWEYIIGFCDQIN-KELEGPQIAVRLLAHKIQSPQEWEAVQALTVLEACMKNCGRRFHNEVGKF 87
Cdd:cd16998     1 LQRYIERACDPSLEEPNLALNLEIADLINeKQGNTPREAAFAIVRLVNSRNPTVALLALHLLDVCVKNCGYPFHLQIASK 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2020834100  88 RFLNELIKVV---SPKYLGdrvseKVKTKVIELLYSWTLALPEETKIKD 133
Cdd:cd16998    81 EFLNELVRRFperPPSRLN-----PVQHKILELIEEWKQTLCKTSRYKE 124
VHS_Vps27 cd16979
VHS (Vps27/Hrs/STAM) domain of Vacuolar protein sorting-associated protein 27; Vacuolar ...
 8-143 7.20e-11

VHS (Vps27/Hrs/STAM) domain of Vacuolar protein sorting-associated protein 27; Vacuolar protein sorting-associated protein 27 (Vps27 or Vps27p) is also called Golgi retention defective protein 11, and is the yeast homolog of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate). Together with class E vacuolar protein-sorting machinery protein HSE1, it comprises the ESCRT-0 complex, the sorting receptor for ubiquitinated cargo proteins at the multivesicular body (MVB). The complex directly binds to ubiquitinated transmembrane proteins and recruits both ubiquitin ligases and deubiquitinating enzymes. It is also required the efficient recycling of late Golgi proteins including the carboxypeptidase Y (CPY) sorting receptor, Vps10. Vps27 contain similar domains and motifs to Hrs; it contains an N-terminal VHS domain, which has a superhelical structure similar to the structure of ARM (Armadillo) repeats, a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain, two Ubiquitin-Interacting Motifs (UIMs), a GAT (GGA and TOM) domain, two a P(S/T)XP motifs that recruit ESCRT-I, and a short peptide motif near the C-terminus that recruits clathrin.


Pssm-ID: 340776  Cd Length: 141  Bit Score: 60.29  E-value: 7.20e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100   8 SLESWLNKATNPS--NRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQS--PQeweaVQ--ALTVLEACMKNCGRRFH 81
Cdd:cd16979     2 EFDELIEKATSESipNGEEDLALALEISDLIRSKSVPPKDAMRSLKKRILHknPN----VQllALKLTDVCVKNGGDHFL 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2020834100  82 NEVGKFRFLNELIKVVspkyLGDRVSEKVKTKVIELLYSWTLAL---PEETKIKDAYHMLKRQGI 143
Cdd:cd16979    78 VEIASREFMDNLVSLI----RSTGVNPEVKEKILRLIQEWALAFkskSQLSYVVEVYKKLKSEGI 138
GGA_N-GAT pfam18308
N-terminal extension of GAT domain; This region is found in the N-terminal region of the GGA ...
 169-207 1.32e-09

N-terminal extension of GAT domain; This region is found in the N-terminal region of the GGA and Tom1 (GAT) domain in Golgi-localizing gamma-adaptin ARF-binding protein 1 (GGA1) present in Homo sapiens. The GAT domain is the key region in GGA that interacts with ARF. ARF plays a crucial role in docking adaptor proteins to membranes. This region is referred to as N-GAT and it interacts extensively with ARF.


Pssm-ID: 465702  Cd Length: 39  Bit Score: 53.85  E-value: 1.32e-09
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2020834100 169 FDDEEKSKLLAKLLKSKNPDDLQEANKLIKSMVKEDEAR 207
Cdd:pfam18308   1 FDDEEKSKLLARLLKSKNPEDLQAANRLIKSMVKEDDER 39
PHA03247 PHA03247
large tegument protein UL36; Provisional
 304-594 5.22e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 53.40  E-value: 5.22e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  304 GEVATSAIPDSEGLADPAPTAP---PTESAGNSQWPLFQNEQLDLDFGGP---------EPGSA--AASPSDGP----LV 365
Cdd:PHA03247  2610 GPAPPSPLPPDTHAPDPPPPSPspaANEPDPHPPPTVPPPERPRDDPAPGrvsrprrarRLGRAaqASSPPQRPrrraAR 2689

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  366 PPSAPSAGSSQAPLPPSFPAPAVPASVPA-PKPGSFLFPTGPAPALKAEPTAlgyHGSALGDSTlhqlDALDHLLEETRA 444
Cdd:PHA03247  2690 PTVGSLTSLADPPPPPPTPEPAPHALVSAtPLPPGPAAARQASPALPAAPAP---PAVPAGPAT----PGGPARPARPPT 2762

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  445 TSGLVKPVSSIFFPG----ATTSPLVPTSTTARPLLPFSPGPSSPlfqPQGSPMKGPELSLASVHVPLESiKPSSALPVT 520
Cdd:PHA03247  2763 TAGPPAPAPPAAPAAgpprRLTRPAVASLSESRESLPSPWDPADP---PAAVLAPAAALPPAASPAGPLP-PPTSAQPTA 2838

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  521 AYDKNGFRILF-----------HFAKECPPGRPdvlvvvVSMLNTAPLPIKSIVLQAAVPKSMKVKLQPPSGTELSPFSP 589
Cdd:PHA03247  2839 PPPPPGPPPPSlplggsvapggDVRRRPPSRSP------AAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQ 2912


                   ....*
gi 2020834100  590 IQPPA 594
Cdd:PHA03247  2913 APPPP 2917
GAT_TOM1_like cd14233
canonical GAT domain found in target of myb protein 1 (Tom1) protein family; Tom1 and its ...
 212-293 3.94e-06

canonical GAT domain found in target of myb protein 1 (Tom1) protein family; Tom1 and its related proteins, Tom1L1 and Tom1L2, form a protein family sharing an N-terminal VHS (Vps27p/Hrs/STAM)-domain followed by a GAT (GGA and TOM1) domain, both of which are also conserved in Golgi-localized gamma ear-containing Arf-binding proteins (GGAs). In contrast to GGAs, the Tom1 family proteins bind to ubiquitin, ubiquitinated proteins, and Toll-interacting protein (Tollip) through its GAT domain, but do not associate with Arf GTPases through its GAT domain nor with acidic cluster-dileucine sequences through its VHS domain. In addition, the Tom1 family proteins recruit clathrin onto endosomes through their C-terminal region. In their C-terminal clathrin-binding regions, Tom1 and Tom1L2 are similar to each other, but distinguishable from Tom1L1. The yeast S. cerevisiae does not contain homologous proteins of the Tom1 family. The canonical GAT domain is a monomeric three-helix bundle that binds ubiquitin.


Pssm-ID: 410581  Cd Length: 87  Bit Score: 45.26  E-value: 3.94e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 212 TKRLHTLEEVNNNVKLLNEMLLHYSKEDSSEADKELMKELFDRCENKRRTLFKLASETeDNDNSLGDILQASDNLSRVIS 291
Cdd:cd14233     2 AKLRSELDVVEGNLKVMSEMLTELVPGQENPDDLELLQELNSTCRAMQQRVVELISQV-SNEEVTEELLRVNDDLNNVFL 80


                  ..
gi 2020834100 292 SY 293
Cdd:cd14233    81 RY 82
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 309-515 5.45e-06

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 49.78  E-value: 5.45e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  309 SAIPDSEGLADPAPTAPPTESAGNSQWPLFQNEQLDLDFGGPEPGSAAASPSDG----PLVPPSAPSAGSSQAPLPPSFP 384
Cdd:PHA03307   119 PTPPPASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQAalplSSPEETARAPSSPPAEPPPSTP 198

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  385 APAVPASVPAPKPGSFLFPTGPAPALkAEPTALGYHGSALGDSTLHQLDALDHLLEETRatsglVKPVSSIFFPGATTSP 464
Cdd:PHA03307   199 PAAASPRPPRRSSPISASASSPAPAP-GRSAADDAGASSSDSSSSESSGCGWGPENECP-----LPRPAPITLPTRIWEA 272

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2020834100  465 LVPTSTTARPLLPFSPGPSSPLfQPQGSPMKGPELSLASVHVPLESIKPSS 515
Cdd:PHA03307   273 SGWNGPSSRPGPASSSSSPRER-SPSPSPSSPGSGPAPSSPRASSSSSSSR 322
PHA03247 PHA03247
large tegument protein UL36; Provisional
 350-594 5.50e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 49.94  E-value: 5.50e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  350 PEPGSAAASPSDGPLVP-PSAPSAGSSQAPLPPSFPAPAVPASVPA-----------PKPGSFLFPTGPA-PALKAEPTA 416
Cdd:PHA03247  2704 PPPTPEPAPHALVSATPlPPGPAAARQASPALPAAPAPPAVPAGPAtpggparparpPTTAGPPAPAPPAaPAAGPPRRL 2783

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  417 LGYHGSALGDSTLHQLDALDhlleeTRATSGLVKPVSSIFFPGATTSPLVPTSTTARPLLP-FSPGPSSPLFQPQGSPMK 495
Cdd:PHA03247  2784 TRPAVASLSESRESLPSPWD-----PADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPpPPPGPPPPSLPLGGSVAP 2858

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  496 GPelslasvhvPLESIKPSSALPvtaydkngfrilfhfAKECPPGRPDVLVVvvsmlnTAPLPIKSIVLQAAVPKSMKVK 575
Cdd:PHA03247  2859 GG---------DVRRRPPSRSPA---------------AKPAAPARPPVRRL------ARPAVSRSTESFALPPDQPERP 2908

                          250
                   ....*....|....*....
gi 2020834100  576 LQPPSGTELSPFSPIQPPA 594
Cdd:PHA03247  2909 PQPQAPPPPQPQPQPPPPP 2927
PHA03247 PHA03247
large tegument protein UL36; Provisional
 307-605 1.90e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 48.01  E-value: 1.90e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  307 ATSAIPDSEGLADPAPTAPPT-----------ESAGNS------QWPLFQNEQLDLDFGGPEPGSAAASPSDGP--LVP- 366
Cdd:PHA03247  2491 AAGAAPDPGGGGPPDPDAPPApsrlapailpdEPVGEPvhprmlTWIRGLEELASDDAGDPPPPLPPAAPPAAPdrSVPp 2570

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  367 ------PSAPSAGSSQA--PLPPSFPAPAVPASVPAPKPGSfLFPTGPAPALKA-EPTALGYHGSALGDSTLHQLDALDH 437
Cdd:PHA03247  2571 prpaprPSEPAVTSRARrpDAPPQSARPRAPVDDRGDPRGP-APPSPLPPDTHApDPPPPSPSPAANEPDPHPPPTVPPP 2649

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  438 LLEETRATSGLVKPVSSIFFPGATTSPLVPTSTTARPLLPFSPGPSSPLFQP---QGSPMKGPELSLASVHVPLESIKPS 514
Cdd:PHA03247  2650 ERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPpppPPTPEPAPHALVSATPLPPGPAAAR 2729

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  515 SALPVTAydkngfrilfhfAKECPPGRPDVLVVVVSMLNTAPLPIKSIVLQAAVPK----SMKVKLQPPSGTELSPFSPI 590
Cdd:PHA03247  2730 QASPALP------------AAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAapaaGPPRRLTRPAVASLSESRES 2797

                          330
                   ....*....|....*....
gi 2020834100  591 QP----PAAITQVMLLANP 605
Cdd:PHA03247  2798 LPspwdPADPPAAVLAPAA 2816
kgd PRK12270
multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine ...
 317-428 3.41e-05

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;


Pssm-ID: 237030 [Multi-domain]  Cd Length: 1228  Bit Score: 47.19  E-value: 3.41e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  317 LADPaptapptESAGNSQWPLFQneqldlDFGGPEPGSAAASPSDGPLVPPSAPSAGSSQAPLPPSFPAPAVPASVPAPK 396
Cdd:PRK12270    19 LADP-------NSVDPSWREFFA------DYGPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPK 85

                           90       100       110
                   ....*....|....*....|....*....|..
gi 2020834100  397 PGSFLFPTGPAPALKAEPTALGYHGSALGDST 428
Cdd:PRK12270    86 PAAAAAAAAAPAAPPAAAAAAAPAAAAVEDEV 117
GAT_TOM1 cd14236
canonical GAT domain found in target of Myb protein 1 (Tom1); Tom1 was originally identified ...
 213-289 4.96e-05

canonical GAT domain found in target of Myb protein 1 (Tom1); Tom1 was originally identified by its induced expression by the v-Myb oncogene. It is predominantly present in the cytosol and can interact with clathrin, endofin, Toll-interacting protein (Tollip), and ubiquitinated proteins. It acts as a linker protein to regulate the ability of endofin to recruit clathrin onto the sorting endosome. Moreover, Tom1 functions as a negative regulator of IL-1beta and tumor necrosis factor (TNF)-alpha-induced signaling pathways. It also plays a role in the TLR2/4 signaling pathways. Tom1 contains an N-terminal VHS (Vps27p/Hrs/STAM)-domain, a GAT (GGA and TOM1) domain and a C-terminal clathrin-binding region, both of which are conserved in Golgi-localized gamma ear-containing Arf-binding proteins (GGAs). In contrast to GGAs, Tom1 binds to ubiquitin, ubiquitinated proteins, and Tollip through its GAT domain, but does not associate with Arf GTPases through its GAT domain nor with acidic cluster-dileucine sequences through its VHS domain. The canonical GAT domain is a monomeric three-helix bundle that binds ubiquitin.


Pssm-ID: 260094  Cd Length: 95  Bit Score: 42.33  E-value: 4.96e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2020834100 213 KRLHT-LEEVNNNVKLLNEMLLHYSKEDSSEADKELMKELFDRCENKRRTLFKLASETEdNDNSLGDILQASDNLSRV 289
Cdd:cd14236     5 GKLRSeLEMVSGNVRVMSEMLTELVPTQAEPADLELLQELNRTCRAMQQRVLELIPQIA-NEQLTEELLIVNDNLNNV 81
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
348-518 6.65e-05

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 46.02  E-value: 6.65e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 348 GGPEPGSAAASPSDGPLVPPSAPSAGSSQAPLPPSFPAPAVPASVPAPKPGSflFPTGPAPALKAEPTALGYHGSALGds 427
Cdd:PRK12323  370 GGAGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAA--APARRSPAPEALAAARQASARGPG-- 445

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 428 tlhqldaldhlleetRATSGLVKPVSSiffPGATTSPLVPTSTTARPLLPFSPGPSSPLFQPQGSPMKGPELSLASVHVP 507
Cdd:PRK12323  446 ---------------GAPAPAPAPAAA---PAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPPPWEELPPEFA 507

                         170
                  ....*....|.
gi 2020834100 508 LESIKPSSALP 518
Cdd:PRK12323  508 SPAPAQPDAAP 518
PHA03247 PHA03247
large tegument protein UL36; Provisional
 346-594 1.23e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 45.70  E-value: 1.23e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  346 DFGGPEPGSAAASPSDGPLVPPSAPSAGSSQAPLPPSFPAPAVPASVPAPKPGSFLFP---TGPAPALKAEPTALGYHGS 422
Cdd:PHA03247  2607 DPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPrraRRLGRAAQASSPPQRPRRR 2686

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  423 ALGDSTLHQLDALDHLLEE-------TRATSGLVKP----VSSIFFPGATTSPLVPTSTTA-----------RPLLPFSP 480
Cdd:PHA03247  2687 AARPTVGSLTSLADPPPPPptpepapHALVSATPLPpgpaAARQASPALPAAPAPPAVPAGpatpggparpaRPPTTAGP 2766

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  481 G-PSSPLFQPQGSPMKGPELSLASVHVPLESI-KPSSALPVTAYDKNGFRILFHFAKECPPGRPDVLVVVVSMLNTAPLP 558
Cdd:PHA03247  2767 PaPAPPAAPAAGPPRRLTRPAVASLSESRESLpSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPP 2846

                          250       260       270
                   ....*....|....*....|....*....|....*..
gi 2020834100  559 IKSIVLQAAVPKSMKVKLQPPSG-TELSPFSPIQPPA 594
Cdd:PHA03247  2847 PPSLPLGGSVAPGGDVRRRPPSRsPAAKPAAPARPPV 2883
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
295-494 2.13e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 44.48  E-value: 2.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 295 TVVEGQVVNGEVATSAIPdsegLADPAPTAPPTESAGNSQWPLFQNEQLDLDfGGPEPGSAAASPSDGPlvPPSAPSAGS 374
Cdd:PRK12323  376 TAAAAPVAQPAPAAAAPA----AAAPAPAAPPAAPAAAPAAAAAARAVAAAP-ARRSPAPEALAAARQA--SARGPGGAP 448

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 375 SQAPLPPSFPAPAVPASVPAPKPGSFLFPTGPAPALKAEPTALGYHGS--------ALGDSTLHQLDALDHLLEETRATS 446
Cdd:PRK12323  449 APAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPppweelppEFASPAPAQPDAAPAGWVAESIPD 528

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2020834100 447 GLVKPVSSIFFPGATTSPLVPTSTTARPLLPFSPGPSSPLFQPQGSPM 494
Cdd:PRK12323  529 PATADPDDAFETLAPAPAAAPAPRAAAATEPVVAPRPPRASASGLPDM 576
half-pint TIGR01645
poly-U binding splicing factor, half-pint family; The proteins represented by this model ...
 309-415 3.76e-04

poly-U binding splicing factor, half-pint family; The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.


Pssm-ID: 130706 [Multi-domain]  Cd Length: 612  Bit Score: 43.52  E-value: 3.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 309 SAIPDSEGLADPAPTAPPTES---AGNS------QWPLFQNEQLDLDFGGPEPGSAAASPSDgpLVPPSAPSAGSSQAPL 379
Cdd:TIGR01645 295 SAIPAAAAVAAAAATAKIMAAeavAGAAvlgpraQSPATPSSSLPTDIGNKAVVSSAKKEAE--EVPPLPQAAPAVVKPG 372

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2020834100 380 PPSFPAPAVPASVPAP---KPGSFLFPTGPAPALKAEPT 415
Cdd:TIGR01645 373 PMEIPTPVPPPGLAIPslvAPPGLVAPTEINPSFLASPR 411
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 347-482 5.74e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 43.16  E-value: 5.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 347 FGGPEPGSAAASPsdgpLVPPSAPSAGSSQAPLPPSFPAPAVP---ASVPAPKPGSFLFPTGPAPALKAEPTALGYHGSA 423
Cdd:PRK14951  368 AAAEAAAPAEKKT----PARPEAAAPAAAPVAQAAAAPAPAAApaaAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAAPA 443

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 424 lgdsTLHQLDALDHLL-EETRATSGLVKPVSsiffPGATTSPLVPTSTTARPLLPFSPGP 482
Cdd:PRK14951  444 ----AVALAPAPPAQAaPETVAIPVRVAPEP----AVASAAPAPAAAPAAARLTPTEEGD 495
GAT_GGA_fungi cd14235
canonical GAT domain found in fungal ADP-ribosylation factor (Arf)-binding proteins (GGAs); ...
 218-299 8.32e-04

canonical GAT domain found in fungal ADP-ribosylation factor (Arf)-binding proteins (GGAs); GGAs, also called Golgi-localized gamma-ear-containing Arf-binding proteins, belong to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. Two GGAs (Gga1p and Gga2p) have been identified in the budding yeast Saccharomyces cerevisiae. Yeast GGAs play important roles in the carboxypeptidase Y (CPY) pathway, vacuole biogenesis, alpha-factor maturation, and interactions with clathrin. They have a multidomain structure consisting of VHS (Vps27/Hrs/ STAM), GAT (GGA and TOM), hinge, and GAE (gamma-adaptin ear) domains. Both Gga1p and Gga2p function as effectors of Arf in yeast. They interact with Arf1p and Arf2p in a GTP-dependent manner. Moreover, Gga2p mediates sequential ubiquitin-independent and ubiquitin-dependent steps in the trafficking of ARN1, a ferrichrome transporter in S. cerevisiae, from the TGN to the vacuole. It also acts as a phosphatidylinositol 4-phosphate effector at the Golgi exit, which binds directly to the TGN PtdIns(4)-kinase Pik1p and contributes to Pik1p recruitment. In addition, Gga2p is required for sorting of the yeast siderophore iron transporter1 (Sit1) to the vacuolar pathway. The GAT domain of GGAs interacts with class I GTP-bound form of Arf proteins, Rabaptin-5, ubiquitin, and/or the tumor susceptibility gene 101 product (TSG101).


Pssm-ID: 410583  Cd Length: 92  Bit Score: 38.75  E-value: 8.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 218 LEEVNNNVKLLNEMLLHYSKEDSSeADKELMKELFDRCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVISSYKTVV 297
Cdd:cd14235    10 LEKLKRKAILLNEMLNNATPGEID-VEGDTYDELASSLKSAQPKIQKIIEEESEDEESVQKLLELNDLINSLLERYDLLK 88


                  ..
gi 2020834100 298 EG 299
Cdd:cd14235    89 KG 90
GAT_TM1L2 cd14238
canonical GAT domain found in target of Myb-like protein 2 (Tom1L2); Tom1L2, together with Myb ...
 209-294 1.00e-03

canonical GAT domain found in target of Myb-like protein 2 (Tom1L2); Tom1L2, together with Myb protein 1 (Tom1) and target of Myb-like protein 1 (Tom1L1), constitute the Tom1 family. Tom1L2 can interact with Toll-interacting protein (Tollip), clathrin, and ubiquitin. It may play a potential role in endosomal sorting, as well as in the regulation of membrane trafficking that is linked to immunity and cell proliferation. Tom1L2 contains an N-terminal VHS (Vps27p/Hrs/STAM)-domain, a GAT (GGA and TOM1) domain, and a C-terminal clathrin-binding region, both of which are conserved in Golgi-localized gamma ear-containing Arf-binding proteins (GGAs). It interacts with Tollip through their GAT domain and recuits clathrin onto endosomes through their C-terminal region. However, in the C-terminal clathrin-binding region, Tom1 and Tom1L2 are similar to each other, but distinguishable from Tom1L1. The canonical GAT domain is a monomeric three-helix bundle that binds ubiquitin.


Pssm-ID: 410585  Cd Length: 92  Bit Score: 38.87  E-value: 1.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 209 QKVTKRLHTLEEVNNNVKLLNEMLLHYSKEDSSEADKELMKELFDRCENKRRTLFKLASETEdNDNSLGDILQASDNLSR 288
Cdd:cd14238     2 EQIARLRSELDIVRGNTKVMSEMLTEMVPGQEDPSDLELLQELNRTCRAMQQRIVELISRVS-NEEVTEELLHVNDDLNN 80


                  ....*.
gi 2020834100 289 VISSYK 294
Cdd:cd14238    81 VFLRYE 86
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
350-521 2.37e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 40.99  E-value: 2.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 350 PEPGSAAASPSDGPLVPPSAPSAGSSQAPLPPSFPAPAVPASVPAPkpgsflfPTGPAPALKAEPTAlgyhGSALGDSTL 429
Cdd:PRK07003  381 PAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAP-------PAAPAPPATADRGD----DAADGDAPV 449

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 430 hQLDALDHLLEETRATSGLVKPVSSiffPGATTSPlvptSTTARPLLPFSPGPSSPLFQPQGSPMKGPELSLASVHVPLE 509
Cdd:PRK07003  450 -PAKANARASADSRCDERDAQPPAD---SGSASAP----ASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASREDA 521

                         170
                  ....*....|..
gi 2020834100 510 SIKPSSALPVTA 521
Cdd:PRK07003  522 PAAAAPPAPEAR 533
PHA03247 PHA03247
large tegument protein UL36; Provisional
 356-435 2.75e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 41.08  E-value: 2.75e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100  356 AASPSDGPLVPPSAPSAGSSQAPLPPSFPAPAVPAS---VPAPKPGSflfPTGPAPALKAEPT--ALGYHGSALGDSTLH 430
Cdd:PHA03247   396 ARGPGGDDQTRPAAPVPASVPTPAPTPVPASAPPPPatpLPSAEPGS---DDGPAPPPERQPPapATEPAPDDPDDATRK 472


                   ....*
gi 2020834100  431 QLDAL 435
Cdd:PHA03247   473 ALDAL 477
COG5373 COG5373
Uncharacterized membrane protein [Function unknown];
350-397 2.86e-03

Uncharacterized membrane protein [Function unknown];


Pssm-ID: 444140 [Multi-domain]  Cd Length: 854  Bit Score: 40.75  E-value: 2.86e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2020834100 350 PEPGSAAASPSDGPLVPPSAPSAGSSQAPLPPSFPAPAVPASVPAPKP 397
Cdd:COG5373    50 PEPEAAAAATAAAPEAAPAPVPEAPAAPPAAAEAPAPAAAAPPAEAEP 97
PRK14959 PRK14959
DNA polymerase III subunits gamma and tau; Provisional
 349-418 2.93e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184923 [Multi-domain]  Cd Length: 624  Bit Score: 40.82  E-value: 2.93e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2020834100 349 GPEPGSAAASPSDGPLVPPSA-------PSAGSSQAPLPPSFPAPAVPASVPAPKPGSFLFPTGPAPALKAEPTALG 418
Cdd:PRK14959  388 GPASGGAATIPTPGTQGPQGTapaagmtPSSAAPATPAPSAAPSPRVPWDDAPPAPPRSGIPPRPAPRMPEASPVPG 464
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
307-422 3.04e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 40.63  E-value: 3.04e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 307 ATSAIPDSEGLADPAPTAPPTESAGNSQWPLFQN----EQLDLDFGGPEPGSAAASPSDGPLVPPSAPSAGSSQAPLPPS 382
Cdd:PRK12323  462 ARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDpppwEELPPEFASPAPAQPDAAPAGWVAESIPDPATADPDDAFETL 541

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2020834100 383 FPAPAvPASVPAPKPGSFLFPTGPAPALKAEPTALGYHGS 422
Cdd:PRK12323  542 APAPA-AAPAPRAAAATEPVVAPRPPRASASGLPDMFDGD 580
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 236-604 3.38e-03

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 40.52  E-value: 3.38e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 236 SKEDS-SEADKELMKELFDRCENKRRTLFKLASETEDNDNSlgdilQASDNLSRVISSYKTVVEGQvvnGEVATSAIPDS 314
Cdd:pfam03154  57 SKAESmKKSSKKIKEEAPSPLKSAKRQREKGASDTEEPERA-----TAKKSKTQEISRPNSPSEGE---GESSDGRSVND 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 315 EGLADPAPTAPPTESAGNSqWPLFQNEQLDLDFGGPEPGSAAASPS----DGPLVPPSAPSAGSSQAPLPPsfPAPAVPA 390
Cdd:pfam03154 129 EGSSDPKDIDQDNRSTSPS-IPSPQDNESDSDSSAQQQILQTQPPVlqaqSGAASPPSPPPPGTTQAATAG--PTPSAPS 205

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 391 SVPAPKPGSFLFPTGPAPAlkAEPTALGYHGSALGDSTL-HQLDALDHLLEETRATSGLVKPVSSIFFPGATtsPLVPTS 469
Cdd:pfam03154 206 VPPQGSPATSQPPNQTQST--AAPHTLIQQTPTLHPQRLpSPHPPLQPMTQPPPPSQVSPQPLPQPSLHGQM--PPMPHS 281

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 470 TTARPLLPFSPGPSSPL-FQPQGSPMKGPELSLASVHVPLESIK----PSSALPvtaydkngfrilfhfaKECPPGRPDV 544
Cdd:pfam03154 282 LQTGPSHMQHPVPPQPFpLTPQSSQSQVPPGPSPAAPGQSQQRIhtppSQSQLQ----------------SQQPPREQPL 345

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2020834100 545 LVVVVSMLNTAPLPIKSIVlQAAVPKSMKvklQPPSGTELSPF---SPIQPPAAITQVMLLAN 604
Cdd:pfam03154 346 PPAPLSMPHIKPPPTTPIP-QLPNPQSHK---HPPHLSGPSPFqmnSNLPPPPALKPLSSLST 404
motB PRK12799
flagellar motor protein MotB; Reviewed
 363-485 4.36e-03

flagellar motor protein MotB; Reviewed


Pssm-ID: 183756 [Multi-domain]  Cd Length: 421  Bit Score: 40.08  E-value: 4.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 363 PLVPPSAPSAGSSQAPLPPSFPAPAVPASVPAPKPGSflfptgPAPALKAEPTALGYHGSALGDSTLHQLDAldhlLEET 442
Cdd:PRK12799  300 PVAAVTPSSAVTQSSAITPSSAAIPSPAVIPSSVTTQ------SATTTQASAVALSSAGVLPSDVTLPGTVA----LPAA 369

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2020834100 443 RATSGLVKPVSSIFFPGATTSPLVPTS---TTARPLLPFSPGPSSP 485
Cdd:PRK12799  370 EPVNMQPQPMSTTETQQSSTGNITSTAngpTTSLPAAPASNIPVSP 415
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 348-423 4.90e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 39.97  E-value: 4.90e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2020834100 348 GGPEPGSAAASPSDGPLVPPSAPSAGSSQAPLPPSFPAPAVPASVPAPKPGSflfPTGPAPALKAEPTALGYHGSA 423
Cdd:PRK07764  384 RLGVAGGAGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAP---APAPAPPSPAGNAPAGGAPSP 456
GAT_GGA-like_plant cd14231
canonical GAT domain found in uncharacterized Golgi-localized gamma ear-containing Arf-binding ...
 223-294 4.93e-03

canonical GAT domain found in uncharacterized Golgi-localized gamma ear-containing Arf-binding protein (GGA)-like proteins mainly found in plants; The family includes a group of uncharacterized plant proteins containing an N-terminal VHS (Vps27p/Hrs/STAM)-domain and a GAT (GGA and TOM1) domain. Both domains are also present in Golgi-localized gamma ear-containing Arf-binding proteins (GGAs), which belong to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. In contrast to GGA proteins, members in this family do not have either a GAE (gamma-adaptin ear homology) domain or a clathrin-binding motif. The canonical GAT domain is a monomeric three-helix bundle that binds ubiquitin.


Pssm-ID: 410579  Cd Length: 79  Bit Score: 36.47  E-value: 4.93e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2020834100 223 NNVKLLNEMLLHYSKEDSSEADKELMKELFDRCENKRRTLFKLASETEDNDnSLGDILQASDNLSRVISSYK 294
Cdd:cd14231     7 NSLELLSDMLNAVDPRDPEALKDELTVDLVEQCRQSQPRVMQLVESTGDEG-LLFQALELNDELQRVLSKHD 77
KLF9_13_N-like cd21975
Kruppel-like factor (KLF) 9, KLF13, KLF14, KLF16, and similar proteins; Kruppel/Krueppel-like ...
 298-423 6.96e-03

Kruppel-like factor (KLF) 9, KLF13, KLF14, KLF16, and similar proteins; Kruppel/Krueppel-like transcription factors (KLFs) belong to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. KLF9, KLF10, KLF11, KLF13, KLF14, and KLF16 share a conserved alpha-helical motif AA/VXXL that mediates their binding to Sin3A and their activities as transcriptional repressors. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the related N-terminal domains of KLF9, KLF13, KLF14, KLF16, and similar proteins.


Pssm-ID: 409240 [Multi-domain]  Cd Length: 163  Bit Score: 37.75  E-value: 6.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 298 EGQVVNGEVATSAIPDSEGLADPAPTAPPTESAGNSQWPLFQNEQLDLDfGGPEPGSAAASPSDGPLV-PPSAPSAGSSQ 376
Cdd:cd21975    32 AGLDVRATREVAKGPGPPGPAWKPDGADSPGLVTAAPHLLAANVLAPLR-GPSVEGSSLESGDADMGSdSDVAPASGAAA 110

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2020834100 377 APLP-PSFPAPAVPASVPAPKPG-SFLFPTGPAPALKAEPTALGYHGSA 423
Cdd:cd21975   111 STSPeSSSDAASSPSPLSLLHPGeAGLEPERPRPRVRRGVRRRGVTPAA 159
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 304-451 6.96e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 39.58  E-value: 6.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 304 GEVATSAIPDSEGlADPAPTAPPTESAGNSQwplfqneqldldfGGPEPGSA---------AASPSDGPLVPPSAPSAGS 374
Cdd:PRK07764  391 AGAPAAAAPSAAA-AAPAAAPAPAAAAPAAA-------------AAPAPAAApqpapapapAPAPPSPAGNAPAGGAPSP 456

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 375 SQAPLPPSFPAPAVPASVPAPKPGSFLFPTGPAPALKAE-PTALGYHGSALGDSTLHQL--DALDHLLEETRATSGLVKP 451
Cdd:PRK07764  457 PPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAaPAAPAAPAGADDAATLRERwpEILAAVPKRSRKTWAILLP 536
PHA02030 PHA02030
hypothetical protein
 338-416 7.81e-03

hypothetical protein


Pssm-ID: 222843 [Multi-domain]  Cd Length: 336  Bit Score: 38.81  E-value: 7.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 338 FQNEQLDLDFGG----PEPGSAAASPSDGPLVPPSAPSAGSSQAPLPPSFPAPAVPASVPAPK-PGSFLFPTGPAPALKA 412
Cdd:PHA02030  238 FPGSALHILLGGgedlIIKPKSKAAGSNLPAVPNVAADAGSAAAPAVPAAAAAVAQAAPSVPQvPNVAVLPDVPQVAPVA 317


                  ....
gi 2020834100 413 EPTA 416
Cdd:PHA02030  318 APAA 321
PRK06549 PRK06549
acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
 348-401 8.72e-03

acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated


Pssm-ID: 235826 [Multi-domain]  Cd Length: 130  Bit Score: 37.10  E-value: 8.72e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2020834100 348 GGPEPGSAAASPSDGPLVPPSAPSAgsSQAPLPPSFPAPAVPASVPAPKPGSFL 401
Cdd:PRK06549   22 GAPAQAAAPAQPASTPVPVPTEASP--QVEAQAPQPAAAAGADAMPSPMPGTIL 73
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 341-508 8.92e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 39.20  E-value: 8.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 341 EQLDLDFG-----GPEPGSAAASPSDGPLVPPSAPSAGSSQAPLPPSFPAPAVPASVPAPkpgsflfPTGPAPALKAEPT 415
Cdd:PRK07764  576 EELGGDWQveavvGPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAA-------PAEASAAPAPGVA 648

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020834100 416 ALGYHGSALGDSTLHQLDALDHLLEETRATSGLVKPVSSIFFPGATTSPLVPTSTTARPLLPFSPGPSSPLFQPQGSPMK 495
Cdd:PRK07764  649 APEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGA 728

                         170
                  ....*....|...
gi 2020834100 496 GPELSLASVHVPL 508
Cdd:PRK07764  729 SAPSPAADDPVPL 741
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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