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Conserved domains on  [gi|74355660|gb|AAI04036|]
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ARL13B protein [Homo sapiens]

Protein Classification

ADP-ribosylation factor-like protein 13( domain architecture ID 10134987)

ADP-ribosylation factor-like protein 13 (Arl13) similar to the small ciliary G protein Arl13b, which is required for cilium biogenesis and sonic hedgehog signaling and is mutated in patients with Joubert syndrome, and binds GTP but is not able to hydrolyze it; the GTPase activity remains unclear

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Arl2l1_Arl13_like cd04161
Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a ...
 23-189 1.03e-100

Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily of the Arf family of small GTPases. Arl2l1 was identified in human cells during a search for the gene(s) responsible for Bardet-Biedl syndrome (BBS). Like Arl6, the identified BBS gene, Arl2l1 is proposed to have cilia-specific functions. Arl13 is found on the X chromosome, but its expression has not been confirmed; it may be a pseudogene.


:

Pssm-ID: 133361 [Multi-domain]  Cd Length: 167  Bit Score: 297.00  E-value: 1.03e-100
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  23 TLLMVGLDNAGKTATAKGIQGEYPEDVAPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSSDEE 102
Cdd:cd04161   1 TLLTVGLDNAGKTTLVSALQGEIPKKVAPTVGFTPTKLRLDKYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVVDSSDDD 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660 103 RMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHKCLCQIEPCSAISGYGKKIDKSIKKG 182
Cdd:cd04161  81 RVQEVKEILRELLQHPRVSGKPILVLANKQDKKNALLGADVIEYLSLEKLVNENKSLCHIEPCSAIEGLGKKIDPSIVEG 160


                ....*..
gi 74355660 183 LYWLLHV 189
Cdd:cd04161 161 LRWLLAA 167
CCDC47 super family cl46382
PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of ...
 199-241 2.70e-03

PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex, formed by CCDC47 and Asterix proteins, acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. CCDC47 is required to maintain the stability of Asterix. CCDC47 is associated with various membrane-associated processes and is component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis. It is also involved in the regulation of calcium ion homeostasis in the ER, being also required for proper protein degradation via the ERAD (ER-associated degradation) pathway.


The actual alignment was detected with superfamily member pfam07946:

Pssm-ID: 480722  Cd Length: 323  Bit Score: 39.47  E-value: 2.70e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 74355660   199 ERIQKETTEQRALEEQEKQERAERVRKLREERKQNEQEQAELD 241
Cdd:pfam07946 271 EKIKKAAEEERAEEAQEKKEEAKKKEREEKLAKLSPEEQRKYE 313
 
Name Accession Description Interval E-value
Arl2l1_Arl13_like cd04161
Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a ...
 23-189 1.03e-100

Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily of the Arf family of small GTPases. Arl2l1 was identified in human cells during a search for the gene(s) responsible for Bardet-Biedl syndrome (BBS). Like Arl6, the identified BBS gene, Arl2l1 is proposed to have cilia-specific functions. Arl13 is found on the X chromosome, but its expression has not been confirmed; it may be a pseudogene.


Pssm-ID: 133361 [Multi-domain]  Cd Length: 167  Bit Score: 297.00  E-value: 1.03e-100
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  23 TLLMVGLDNAGKTATAKGIQGEYPEDVAPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSSDEE 102
Cdd:cd04161   1 TLLTVGLDNAGKTTLVSALQGEIPKKVAPTVGFTPTKLRLDKYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVVDSSDDD 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660 103 RMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHKCLCQIEPCSAISGYGKKIDKSIKKG 182
Cdd:cd04161  81 RVQEVKEILRELLQHPRVSGKPILVLANKQDKKNALLGADVIEYLSLEKLVNENKSLCHIEPCSAIEGLGKKIDPSIVEG 160


                ....*..
gi 74355660 183 LYWLLHV 189
Cdd:cd04161 161 LRWLLAA 167
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
 24-190 1.05e-43

ADP-ribosylation factor family; Pfam combines a number of different Prosite families together


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 150.07  E-value: 1.05e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660    24 LLMVGLDNAGKTATAKGIQGEYPEDVAPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSSDEER 103
Cdd:pfam00025   3 ILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADRDR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660   104 MEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHkclCQIEPCSAISGYGkkidksIKKGL 183
Cdd:pfam00025  83 IEEAKEELHALLNEEELADAPLLILANKQDLPGAMSEAEIRELLGLHELKDRP---WEIQGCSAVTGEG------LDEGL 153


                  ....*..
gi 74355660   184 YWLLHVI 190
Cdd:pfam00025 154 DWLSNYI 160
ARF smart00177
ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ...
 20-186 3.27e-28

ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop).


Pssm-ID: 128474 [Multi-domain]  Cd Length: 175  Bit Score: 109.63  E-value: 3.27e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660     20 RKVTLLMVGLDNAGKTATAKGIQ-GEYPEDVaPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDS 98
Cdd:smart00177  12 KEMRILMVGLDAAGKTTILYKLKlGESVTTI-PTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVDS 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660     99 SDEERMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHkclCQIEPCSAISGYGkkidks 178
Cdd:smart00177  91 NDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKLGLHSIRDRN---WYIQPTCATSGDG------ 161


                   ....*...
gi 74355660    179 IKKGLYWL 186
Cdd:smart00177 162 LYEGLTWL 169
PTZ00133 PTZ00133
ADP-ribosylation factor; Provisional
 20-186 4.11e-28

ADP-ribosylation factor; Provisional


Pssm-ID: 173423  Cd Length: 182  Bit Score: 109.55  E-value: 4.11e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660   20 RKVTLLMVGLDNAGKTATAKGIQ-GEYPEDVaPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDS 98
Cdd:PTZ00133  16 KEVRILMVGLDAAGKTTILYKLKlGEVVTTI-PTIGFNVETVEYKNLKFTMWDVGGQDKLRPLWRHYYQNTNGLIFVVDS 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660   99 SDEERMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHkclCQIEPCSAISGYGkkidks 178
Cdd:PTZ00133  95 NDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMSTTEVTEKLGLHSVRQRN---WYIQGCCATTAQG------ 165


                 ....*...
gi 74355660  179 IKKGLYWL 186
Cdd:PTZ00133 166 LYEGLDWL 173
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 24-137 6.69e-14

small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model. [Unknown function, General]


Pssm-ID: 272973 [Multi-domain]  Cd Length: 162  Bit Score: 68.94  E-value: 6.69e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660    24 LLMVGLDNAGKTAT------AKGIQGEYPEDVAPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVD 97
Cdd:TIGR00231   4 IVIVGHPNVGKSTLlnsllgNKGSITEYYPGTTRNYVTTVIEEDGKTYKFNLLDTAGQEDYDAIRRLYYPQVERSLRVFD 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 74355660    98 -SSDEERMEETKEAMSEMLRHPRISGKPILVLANKQDKEGA 137
Cdd:TIGR00231  84 iVILVLDVEEILEKQTKEIIHHADSGVPIILVGNKIDLKDA 124
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
20-172 3.19e-13

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 67.70  E-value: 3.19e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  20 RKVTLLMVGLDNAGKTATAKGIQGEY--PEDVAPTVG----FSKINLRQGKFEVTIFDLGGGIRIRGIWKNY---YAESY 90
Cdd:COG1100   2 GEKKIVVVGTGGVGKTSLVNRLVGDIfsLEKYLSTNGvtidKKELKLDGLDVDLVIWDTPGQDEFRETRQFYarqLTGAS 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  91 GVIFVVDSSDEERMEETKEAMSEMLRHPRISgkPILVLANKQDKegaLGEADVIECLSLEKLVNEHKCLCQIePCSAISG 170
Cdd:COG1100  82 LYLFVVDGTREETLQSLYELLESLRRLGKKS--PIILVLNKIDL---YDEEEIEDEERLKEALSEDNIVEVV-ATSAKTG 155


                ..
gi 74355660 171 YG 172
Cdd:COG1100 156 EG 157
CCDC47 pfam07946
PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of ...
 199-241 2.70e-03

PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex, formed by CCDC47 and Asterix proteins, acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. CCDC47 is required to maintain the stability of Asterix. CCDC47 is associated with various membrane-associated processes and is component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis. It is also involved in the regulation of calcium ion homeostasis in the ER, being also required for proper protein degradation via the ERAD (ER-associated degradation) pathway.


Pssm-ID: 462322  Cd Length: 323  Bit Score: 39.47  E-value: 2.70e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 74355660   199 ERIQKETTEQRALEEQEKQERAERVRKLREERKQNEQEQAELD 241
Cdd:pfam07946 271 EKIKKAAEEERAEEAQEKKEEAKKKEREEKLAKLSPEEQRKYE 313
rne PRK10811
ribonuclease E; Reviewed
 198-259 5.21e-03

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 39.25  E-value: 5.21e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 74355660   198 NERIQKETTEQ-RALEEQEKQERAERVRKLREERKQNEQEQAEL--DGTSGLAELDPEPTNPFQP 259
Cdd:PRK10811  654 RESQQAEVTEKaRTQDEQQQAPRRERQRRRNDEKRQAQQEAKALnvEEQSVQETEQEERVQQVQP 718
 
Name Accession Description Interval E-value
Arl2l1_Arl13_like cd04161
Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a ...
 23-189 1.03e-100

Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily of the Arf family of small GTPases. Arl2l1 was identified in human cells during a search for the gene(s) responsible for Bardet-Biedl syndrome (BBS). Like Arl6, the identified BBS gene, Arl2l1 is proposed to have cilia-specific functions. Arl13 is found on the X chromosome, but its expression has not been confirmed; it may be a pseudogene.


Pssm-ID: 133361 [Multi-domain]  Cd Length: 167  Bit Score: 297.00  E-value: 1.03e-100
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  23 TLLMVGLDNAGKTATAKGIQGEYPEDVAPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSSDEE 102
Cdd:cd04161   1 TLLTVGLDNAGKTTLVSALQGEIPKKVAPTVGFTPTKLRLDKYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVVDSSDDD 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660 103 RMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHKCLCQIEPCSAISGYGKKIDKSIKKG 182
Cdd:cd04161  81 RVQEVKEILRELLQHPRVSGKPILVLANKQDKKNALLGADVIEYLSLEKLVNENKSLCHIEPCSAIEGLGKKIDPSIVEG 160


                ....*..
gi 74355660 183 LYWLLHV 189
Cdd:cd04161 161 LRWLLAA 167
Arf_Arl cd00878
ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl ...
 24-188 6.62e-64

ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thus, despite their significant sequence homologies, Arf family proteins may regulate unrelated functions.


Pssm-ID: 206644 [Multi-domain]  Cd Length: 158  Bit Score: 202.42  E-value: 6.62e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  24 LLMVGLDNAGKTATAKGIQGEYPEDVAPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSSDEER 103
Cdd:cd00878   2 ILMLGLDGAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNVKFTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSSDRER 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660 104 MEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLvneHKCLCQIEPCSAISGYGkkidksIKKGL 183
Cdd:cd00878  82 IEEAKNELHKLLNEEELKGAPLLILANKQDLPGALTESELIELLGLESI---KGRRWHIQPCSAVTGDG------LDEGL 152


                ....*
gi 74355660 184 YWLLH 188
Cdd:cd00878 153 DWLIE 157
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
 24-190 1.05e-43

ADP-ribosylation factor family; Pfam combines a number of different Prosite families together


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 150.07  E-value: 1.05e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660    24 LLMVGLDNAGKTATAKGIQGEYPEDVAPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSSDEER 103
Cdd:pfam00025   3 ILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADRDR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660   104 MEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHkclCQIEPCSAISGYGkkidksIKKGL 183
Cdd:pfam00025  83 IEEAKEELHALLNEEELADAPLLILANKQDLPGAMSEAEIRELLGLHELKDRP---WEIQGCSAVTGEG------LDEGL 153


                  ....*..
gi 74355660   184 YWLLHVI 190
Cdd:pfam00025 154 DWLSNYI 160
Arfrp1 cd04160
Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a ...
 25-186 1.15e-42

Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development.


Pssm-ID: 206725 [Multi-domain]  Cd Length: 168  Bit Score: 147.87  E-value: 1.15e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  25 LMVGLDNAGKTATAKGIQGEY--------PEDVAPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVV 96
Cdd:cd04160   3 LILGLDNAGKTTFLEQTKTKFsknykglnPSKITPTVGLNIGTIEVGKARLMFWDLGGQEELRSLWDKYYAESHGVIYVI 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  97 DSSDEERMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLeKLVNEHKCLCQIEPCSAISGYGkkid 176
Cdd:cd04160  83 DSTDRERFNESKSAFEKVINNEALEGVPLLVLANKQDLPDALSVAEIKEVFDD-CIALIGRRDCLVQPVSALEGEG---- 157

                       170
                ....*....|
gi 74355660 177 ksIKKGLYWL 186
Cdd:cd04160 158 --VEEGIEWL 165
Arl2 cd04154
Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind ...
 20-187 9.41e-40

Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind GDP and GTP with very low affinity. Unlike most Arf family proteins, Arl2 is not myristoylated at its N-terminal helix. The protein PDE-delta, first identified in photoreceptor rod cells, binds specifically to Arl2 and is structurally very similar to RhoGDI. Despite the high structural similarity between Arl2 and Rho proteins and between PDE-delta and RhoGDI, the interactions between the GTPases and their effectors are very different. In its GTP bound form, Arl2 interacts with the protein Binder of Arl2 (BART), and the complex is believed to play a role in mitochondrial adenine nucleotide transport. In its GDP bound form, Arl2 interacts with tubulin- folding Cofactor D; this interaction is believed to play a role in regulation of microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis.


Pssm-ID: 206720 [Multi-domain]  Cd Length: 173  Bit Score: 140.15  E-value: 9.41e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  20 RKVTLLMVGLDNAGKTATAKGIQGEYPEDVAPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSS 99
Cdd:cd04154  13 REMRILMLGLDNAGKTTILKKFNGEDISTISPTLGFNIKTLEYNGYKLNIWDVGGQKSLRSYWRNYFESTDALIWVVDSS 92

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660 100 DEERMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHKCLCqiePCSAISGYGkkidksI 179
Cdd:cd04154  93 DRARLEDCKRELQKLLVEERLAGATLLIFANKQDLPGALSPEEIREVLELDSIKSHHWRIF---GCSAVTGEN------L 163


                ....*...
gi 74355660 180 KKGLYWLL 187
Cdd:cd04154 164 LDGIDWLV 171
Arl6 cd04157
Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small ...
 23-186 3.68e-37

Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small GTPases. Arl6 expression is limited to the brain and kidney in adult mice, but it is expressed in the neural plate and somites during embryogenesis, suggesting a possible role for Arl6 in early development. Arl6 is also believed to have a role in cilia or flagella function. Several proteins have been identified that bind Arl6, including Arl6 interacting protein (Arl6ip), and SEC61beta, a subunit of the heterotrimeric conducting channel SEC61p. Based on Arl6 binding to these effectors, Arl6 is also proposed to play a role in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation. At least three specific homozygous Arl6 mutations in humans have been found to cause Bardet-Biedl syndrome, a disorder characterized by obesity, retinopathy, polydactyly, renal and cardiac malformations, learning disabilities, and hypogenitalism. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily.


Pssm-ID: 206722 [Multi-domain]  Cd Length: 162  Bit Score: 132.94  E-value: 3.68e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  23 TLLMVGLDNAGKTATAKGIQGEYP--EDVAPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSSD 100
Cdd:cd04157   1 NILVLGLDNSGKTTIINQLKPSNAqsQNIVPTVGFNVESFKKGNLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSD 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660 101 EERMEETKEAMSEMLRHPRISGK--PILVLANKQDKEGALGEADVIECLSLEklvNEHKCLCQIEPCSAISGYGkkidks 178
Cdd:cd04157  81 RLRMVVAKDELELLLNHPDIKHRriPILFYANKMDLPDALTAVKITQLLCLE---NIKDKPWHIFASSALTGEG------ 151


                ....*...
gi 74355660 179 IKKGLYWL 186
Cdd:cd04157 152 LDEGVDWL 159
Arl3 cd04155
Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most ...
 13-186 4.04e-37

Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.


Pssm-ID: 206721 [Multi-domain]  Cd Length: 174  Bit Score: 133.29  E-value: 4.04e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  13 KRWREPVRKVTLLMVGLDNAGKTATAKGIQGEYPEDVAPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGV 92
Cdd:cd04155   7 KLKPSSRQEVRILLLGLDNAGKTTILKQLASEDISHITPTQGFNIKNVQADGFKLNVWDIGGQRKIRPYWRNYFENTDVL 86

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  93 IFVVDSSDEERMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEhkcLCQIEPCSAISGYG 172
Cdd:cd04155  87 IYVIDSADRKRFEEAGQELVELLEEEKLAGVPVLVFANKQDLLTAAPAEEVAEALNLHDIRDR---SWHIQACSAKTGEG 163

                       170
                ....*....|....
gi 74355660 173 kkidksIKKGLYWL 186
Cdd:cd04155 164 ------LQEGMNWV 171
Arl1 cd04151
ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi ...
 24-186 1.11e-33

ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi complex, where it is believed to recruit effector proteins to the trans-Golgi network. Like most members of the Arf family, Arl1 is myristoylated at its N-terminal helix and mutation of the myristoylation site disrupts Golgi targeting. In humans, the Golgi-localized proteins golgin-97 and golgin-245 have been identified as Arl1 effectors. Golgins are large coiled-coil proteins found in the Golgi, and these golgins contain a C-terminal GRIP domain, which is the site of Arl1 binding. Additional Arl1 effectors include the GARP (Golgi-associated retrograde protein)/VFT (Vps53) vesicle-tethering complex and Arfaptin 2. Arl1 is not required for exocytosis, but appears necessary for trafficking from the endosomes to the Golgi. In Drosophila zygotes, mutation of Arl1 is lethal, and in the host-bloodstream form of Trypanosoma brucei, Arl1 is essential for viability.


Pssm-ID: 206718 [Multi-domain]  Cd Length: 158  Bit Score: 123.67  E-value: 1.11e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  24 LLMVGLDNAGKTATAKGIQ-GEYPEDVaPTVGFS--KINLRQGKFEVtiFDLGGGIRIRGIWKNYYAESYGVIFVVDSSD 100
Cdd:cd04151   2 ILILGLDGAGKTTILYRLQvGEVVTTI-PTIGFNveTVTYKNLKFQV--WDLGGQTSIRPYWRCYYSNTDAIIYVVDSTD 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660 101 EERMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHkclCQIEPCSAISGYGkkidksIK 180
Cdd:cd04151  79 RDRLGISKSELHAMLEEEELKDAVLLVFANKQDMPGALSEAEVAEKLGLSELKDRT---WQIFKTSATKGEG------LD 149


                ....*.
gi 74355660 181 KGLYWL 186
Cdd:cd04151 150 EGMDWL 155
Arl5_Arl8 cd04153
Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like ...
 11-188 1.28e-32

Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like Arl4 and Arl7, are localized to the nucleus and nucleolus. Arl5 is developmentally regulated during embryogenesis in mice. Human Arl5 interacts with the heterochromatin protein 1-alpha (HP1alpha), a nonhistone chromosomal protein that is associated with heterochromatin and telomeres, and prevents telomere fusion. Arl5 may also play a role in embryonic nuclear dynamics and/or signaling cascades. Arl8 was identified from a fetal cartilage cDNA library. It is found in brain, heart, lung, cartilage, and kidney. No function has been assigned for Arl8 to date.


Pssm-ID: 133353 [Multi-domain]  Cd Length: 174  Bit Score: 121.30  E-value: 1.28e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  11 WFKRWREPVRKVtlLMVGLDNAGKTATAKGIQGEYPEDVAPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESY 90
Cdd:cd04153   7 WSLFFPRKEYKV--IIVGLDNAGKTTILYQFLLGEVVHTSPTIGSNVEEIVYKNIRFLMWDIGGQESLRSSWNTYYTNTD 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  91 GVIFVVDSSDEERMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKlVNEHKclCQIEPCSAISG 170
Cdd:cd04153  85 AVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKGAMTPAEISESLGLTS-IRDHT--WHIQGCCALTG 161

                       170
                ....*....|....*...
gi 74355660 171 ygkkidKSIKKGLYWLLH 188
Cdd:cd04153 162 ------EGLPEGLDWIAS 173
ARLTS1 cd04156
Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), ...
 24-172 2.31e-32

Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), also known as Arl11, is a member of the Arf family of small GTPases that is believed to play a major role in apoptotic signaling. ARLTS1 is widely expressed and functions as a tumor suppressor gene in several human cancers. ARLTS1 is a low-penetrance suppressor that accounts for a small percentage of familial melanoma or familial chronic lymphocytic leukemia (CLL). ARLTS1 inactivation seems to occur most frequently through biallelic down-regulation by hypermethylation of the promoter. In breast cancer, ARLTS1 alterations were typically a combination of a hypomorphic polymorphism plus loss of heterozygosity. In a case of thyroid adenoma, ARLTS1 alterations were polymorphism plus promoter hypermethylation. The nonsense polymorphism Trp149Stop occurs with significantly greater frequency in familial cancer cases than in sporadic cancer cases, and the Cys148Arg polymorphism is associated with an increase in high-risk familial breast cancer.


Pssm-ID: 133356 [Multi-domain]  Cd Length: 160  Bit Score: 120.21  E-value: 2.31e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  24 LLMVGLDNAGKTATAKGIQGEYPEDVAPTVGFSKINLR-QGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSSDEE 102
Cdd:cd04156   2 VLLLGLDSAGKSTLLYKLKHAELVTTIPTVGFNVEMLQlEKHLSLTVWDVGGQEKMRTVWKCYLENTDGLVYVVDSSDEA 81

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660 103 RMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHKclCQIEPCSAISGYG 172
Cdd:cd04156  82 RLDESQKELKHILKNEHIKGVPVVLLANKQDLPGALTAEEITRRFKLKKYCSDRD--WYVQPCSAVTGEG 149
Sar1 cd00879
Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII ...
 23-186 2.55e-31

Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII vesicle coats involved in export of cargo from the ER. The GTPase activity of Sar1 functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER. Activation of the GDP to the GTP-bound form of Sar1 involves the membrane-associated guanine nucleotide exchange factor (GEF) Sec12. Sar1 is unlike all Ras superfamily GTPases that use either myristoyl or prenyl groups to direct membrane association and function, in that Sar1 lacks such modification. Instead, Sar1 contains a unique nine-amino-acid N-terminal extension. This extension contains an evolutionarily conserved cluster of bulky hydrophobic amino acids, referred to as the Sar1-N-terminal activation recruitment (STAR) motif. The STAR motif mediates the recruitment of Sar1 to ER membranes and facilitates its interaction with mammalian Sec12 GEF leading to activation.


Pssm-ID: 206645 [Multi-domain]  Cd Length: 191  Bit Score: 118.15  E-value: 2.55e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  23 TLLMVGLDNAGKTATAKGIQGEYPEDVAPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSSDEE 102
Cdd:cd00879  21 KIVFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELTIGNVKFTTFDLGGHEQARRVWKDYFPEVDGIVFLVDAADPE 100

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660 103 RMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHKCLCQIEP---------CSAISGYGk 173
Cdd:cd00879 101 RFQESKEELDSLLNDEELANVPILILGNKIDKPGAVSEEELREALGLYGTTTGKGGVSLKVSnirpvevfmCSVVKRQG- 179

                       170
                ....*....|...
gi 74355660 174 kidksIKKGLYWL 186
Cdd:cd00879 180 -----YGEGFRWL 187
Arl9_Arfrp2_like cd04162
Arf-like 9 (Arl9)/Arfrp2-like GTPase; Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first ...
 24-169 2.11e-30

Arf-like 9 (Arl9)/Arfrp2-like GTPase; Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first identified as part of the Human Cancer Genome Project. It maps to chromosome 4q12 and is sometimes referred to as Arfrp2 (Arf-related protein 2). This is a novel subfamily identified in human cancers that is uncharacterized to date.


Pssm-ID: 133362 [Multi-domain]  Cd Length: 164  Bit Score: 114.85  E-value: 2.11e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  24 LLMVGLDNAGKTATAKGIQGEYP-EDVAPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSSDEE 102
Cdd:cd04162   2 ILVLGLDGAGKTSLLHSLSSERSlESVVPTTGFNSVAIPTQDAIMELLEIGGSQNLRKYWKRYLSGSQGLIFVVDSADSE 81

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 74355660 103 RMEETKEAMSEMLRHPriSGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHKCLCQiePCSAIS 169
Cdd:cd04162  82 RLPLARQELHQLLQHP--PDLPLVVLANKQDLPAARSVQEIHKELELEPIARGRRWILQ--GTSLDD 144
Arl10_like cd04159
Arf-like 9 (Arl9) and 10 (Arl10) GTPases; Arl10-like subfamily. Arl9/Arl10 was identified from ...
 26-187 6.52e-29

Arf-like 9 (Arl9) and 10 (Arl10) GTPases; Arl10-like subfamily. Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved.


Pssm-ID: 206724 [Multi-domain]  Cd Length: 159  Bit Score: 110.87  E-value: 6.52e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  26 MVGLDNAGKTATAKGIQ-GEYPEDVAPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSSDEERM 104
Cdd:cd04159   4 LVGLQNSGKTTLVNVIAsGQFSEDTIPTVGFNMRKVTKGNVTIKVWDLGGQPRFRSMWERYCRGVNAIVYVVDAADREKL 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660 105 EETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHKClcqiepCSAISGygkKIDKSIKKGLY 184
Cdd:cd04159  84 EVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALSVDELIEQMNLKSITDREVS------CYSISA---KEKTNIDIVLD 154


                ...
gi 74355660 185 WLL 187
Cdd:cd04159 155 WLI 157
Arf6 cd04149
ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins ...
 20-186 8.18e-29

ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins localize to the plasma membrane, where they perform a wide variety of functions. In its active, GTP-bound form, Arf6 is involved in cell spreading, Rac-induced formation of plasma membrane ruffles, cell migration, wound healing, and Fc-mediated phagocytosis. Arf6 appears to change the actin structure at the plasma membrane by activating Rac, a Rho family protein involved in membrane ruffling. Arf6 is required for and enhances Rac formation of ruffles. Arf6 can regulate dendritic branching in hippocampal neurons, and in yeast it localizes to the growing bud, where it plays a role in polarized growth and bud site selection. In leukocytes, Arf6 is required for chemokine-stimulated migration across endothelial cells. Arf6 also plays a role in down-regulation of beta2-adrenergic receptors and luteinizing hormone receptors by facilitating the release of sequestered arrestin to allow endocytosis. Arf6 is believed to function at multiple sites on the plasma membrane through interaction with a specific set of GEFs, GAPs, and effectors. Arf6 has been implicated in breast cancer and melanoma cell invasion, and in actin remodelling at the invasion site of Chlamydia infection.


Pssm-ID: 206716  Cd Length: 168  Bit Score: 111.02  E-value: 8.18e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  20 RKVTLLMVGLDNAGKTATAKGIQGEYPEDVAPTVGFS--KINLRQGKFEVtiFDLGGGIRIRGIWKNYYAESYGVIFVVD 97
Cdd:cd04149   8 KEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNveTVTYKNVKFNV--WDVGGQDKIRPLWRHYYTGTQGLIFVVD 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  98 SSDEERMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHKClcqIEPCSAISGYGkkidk 177
Cdd:cd04149  86 SADRDRIDEARQELHRIINDREMRDALLLVFANKQDLPDAMKPHEIQEKLGLTRIRDRNWY---VQPSCATSGDG----- 157


                ....*....
gi 74355660 178 sIKKGLYWL 186
Cdd:cd04149 158 -LYEGLTWL 165
ARF smart00177
ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ...
 20-186 3.27e-28

ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop).


Pssm-ID: 128474 [Multi-domain]  Cd Length: 175  Bit Score: 109.63  E-value: 3.27e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660     20 RKVTLLMVGLDNAGKTATAKGIQ-GEYPEDVaPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDS 98
Cdd:smart00177  12 KEMRILMVGLDAAGKTTILYKLKlGESVTTI-PTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVDS 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660     99 SDEERMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHkclCQIEPCSAISGYGkkidks 178
Cdd:smart00177  91 NDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKLGLHSIRDRN---WYIQPTCATSGDG------ 161


                   ....*...
gi 74355660    179 IKKGLYWL 186
Cdd:smart00177 162 LYEGLTWL 169
Arf1_5_like cd04150
ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like ...
 22-186 3.60e-28

ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and related proteins. Arfs1-5 are soluble proteins that are crucial for assembling coat proteins during vesicle formation. Each contains an N-terminal myristoylated amphipathic helix that is folded into the protein in the GDP-bound state. GDP/GTP exchange exposes the helix, which anchors to the membrane. Following GTP hydrolysis, the helix dissociates from the membrane and folds back into the protein. A general feature of Arf1-5 signaling may be the cooperation of two Arfs at the same site. Arfs1-5 are generally considered to be interchangeable in function and location, but some specific functions have been assigned. Arf1 localizes to the early/cis-Golgi, where it is activated by GBF1 and recruits the coat protein COPI. It also localizes to the trans-Golgi network (TGN), where it is activated by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA proteins. Humans, but not rodents and other lower eukaryotes, lack Arf2. Human Arf3 shares 96% sequence identity with Arf1 and is believed to generally function interchangeably with Arf1. Human Arf4 in the activated (GTP-bound) state has been shown to interact with the cytoplasmic domain of epidermal growth factor receptor (EGFR) and mediate the EGF-dependent activation of phospholipase D2 (PLD2), leading to activation of the activator protein 1 (AP-1) transcription factor. Arf4 has also been shown to recognize the C-terminal sorting signal of rhodopsin and regulate its incorporation into specialized post-Golgi rhodopsin transport carriers (RTCs). There is some evidence that Arf5 functions at the early-Golgi and the trans-Golgi to affect Golgi-associated alpha-adaptin homology Arf-binding proteins (GGAs).


Pssm-ID: 206717 [Multi-domain]  Cd Length: 159  Bit Score: 108.65  E-value: 3.60e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  22 VTLLMVGLDNAGKTATAKGIQ-GEYPEDVaPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSSD 100
Cdd:cd04150   1 MRILMVGLDAAGKTTILYKLKlGEIVTTI-PTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSND 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660 101 EERMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHkclCQIEPCSAISGYGkkidksIK 180
Cdd:cd04150  80 RERIGEAREELQRMLNEDELRDAVLLVFANKQDLPNAMSAAEVTDKLGLHSLRNRN---WYIQATCATSGDG------LY 150


                ....*.
gi 74355660 181 KGLYWL 186
Cdd:cd04150 151 EGLDWL 156
PTZ00133 PTZ00133
ADP-ribosylation factor; Provisional
 20-186 4.11e-28

ADP-ribosylation factor; Provisional


Pssm-ID: 173423  Cd Length: 182  Bit Score: 109.55  E-value: 4.11e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660   20 RKVTLLMVGLDNAGKTATAKGIQ-GEYPEDVaPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDS 98
Cdd:PTZ00133  16 KEVRILMVGLDAAGKTTILYKLKlGEVVTTI-PTIGFNVETVEYKNLKFTMWDVGGQDKLRPLWRHYYQNTNGLIFVVDS 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660   99 SDEERMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHkclCQIEPCSAISGYGkkidks 178
Cdd:PTZ00133  95 NDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMSTTEVTEKLGLHSVRQRN---WYIQGCCATTAQG------ 165


                 ....*...
gi 74355660  179 IKKGLYWL 186
Cdd:PTZ00133 166 LYEGLDWL 173
PLN00223 PLN00223
ADP-ribosylation factor; Provisional
 20-192 1.84e-27

ADP-ribosylation factor; Provisional


Pssm-ID: 165788  Cd Length: 181  Bit Score: 107.74  E-value: 1.84e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660   20 RKVTLLMVGLDNAGKTATAKGIQ-GEYPEDVaPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDS 98
Cdd:PLN00223  16 KEMRILMVGLDAAGKTTILYKLKlGEIVTTI-PTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDS 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660   99 SDEERMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHkclCQIEPCSAISGYGkkidks 178
Cdd:PLN00223  95 NDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRQRH---WYIQSTCATSGEG------ 165

                        170
                 ....*....|....
gi 74355660  179 IKKGLYWLLHVIAR 192
Cdd:PLN00223 166 LYEGLDWLSNNIAN 179
Arl4_Arl7 cd04152
Arf-like 4 (Arl4) and 7 (Arl7) GTPases; Arl4 (Arf-like 4) is highly expressed in testicular ...
 24-172 3.70e-25

Arf-like 4 (Arl4) and 7 (Arl7) GTPases; Arl4 (Arf-like 4) is highly expressed in testicular germ cells, and is found in the nucleus and nucleolus. In mice, Arl4 is developmentally expressed during embryogenesis, and a role in somite formation and central nervous system differentiation has been proposed. Arl7 has been identified as the only Arf/Arl protein to be induced by agonists of liver X-receptor and retinoid X-receptor and by cholesterol loading in human macrophages. Arl7 is proposed to play a role in transport between a perinuclear compartment and the plasma membrane, apparently linked to the ABCA1-mediated cholesterol secretion pathway. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily.


Pssm-ID: 206719 [Multi-domain]  Cd Length: 183  Bit Score: 101.42  E-value: 3.70e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  24 LLMVGLDNAGKTATAKGIQ-GEYPEDVaPTVGFS--KINLRQGKFEVTIF---DLGGGIRIRGIWKNYYAESYGVIFVVD 97
Cdd:cd04152   6 IVMLGLDSAGKTTVLYRLKfNEFVNTV-PTKGFNteKIKVSLGNAKGVTFhfwDVGGQEKLRPLWKSYTRCTDGIVFVVD 84

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 74355660  98 SSDEERMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEhkCLCQIEPCSAISGYG 172
Cdd:cd04152  85 SVDVERMEEAKTELHKITKFSENQGVPVLVLANKQDLPNALPVSEVEKLLALHELSSS--TPWHVQPACAIIGEG 157
SAR smart00178
Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene ...
 24-190 5.48e-22

Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene required for transport of secretory proteins from the endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 197556 [Multi-domain]  Cd Length: 184  Bit Score: 92.69  E-value: 5.48e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660     24 LLMVGLDNAGKTATAKGIQGEYPEDVAPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSSDEER 103
Cdd:smart00178  20 ILFLGLDNAGKTTLLHMLKNDRLAQHQPTQHPTSEELAIGNIKFTTFDLGGHQQARRLWKDYFPEVNGIVYLVDAYDKER 99

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660    104 MEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLEKLVNEHKCLCQ----IEPCSAI--SGYGkkidk 177
Cdd:smart00178 100 FAESKRELDALLSDEELATVPFLILGNKIDAPYAASEDELRYALGLTNTTTGKGKVGVrpveVFMCSVVrrMGYG----- 174

                          170
                   ....*....|...
gi 74355660    178 sikKGLYWLLHVI 190
Cdd:smart00178 175 ---EGFKWLSQYI 184
ARD1 cd04158
(ADP-ribosylation factor domain protein 1 (ARD1); ARD1 (ADP-ribosylation factor domain protein ...
 20-186 1.32e-21

(ADP-ribosylation factor domain protein 1 (ARD1); ARD1 (ADP-ribosylation factor domain protein 1) is an unusual member of the Arf family. In addition to the C-terminal Arf domain, ARD1 has an additional 46-kDa N-terminal domain that contains a RING finger domain, two predicted B-Boxes, and a coiled-coil protein interaction motif. This domain belongs to the TRIM (tripartite motif) or RBCC (RING, B-Box, coiled-coil) family. Like most Arfs, the ARD1 Arf domain lacks detectable GTPase activity. However, unlike most Arfs, the full-length ARD1 protein has significant GTPase activity due to the GAP (GTPase-activating protein) activity exhibited by the 46-kDa N-terminal domain. The GAP domain of ARD1 is specific for its own Arf domain and does not bind other Arfs. The rate of GDP dissociation from the ARD1 Arf domain is slowed by the adjacent 15 amino acids, which act as a GDI (GDP-dissociation inhibitor) domain. ARD1 is ubiquitously expressed in cells and localizes to the Golgi and to the lysosomal membrane. Two Tyr-based motifs in the Arf domain are responsible for Golgi localization, while the GAP domain controls lysosomal localization.


Pssm-ID: 206723 [Multi-domain]  Cd Length: 169  Bit Score: 91.24  E-value: 1.32e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  20 RKVTLlmvGLDNAGKTATA-KGIQGEYPEDVaPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDS 98
Cdd:cd04158   1 RVVTL---GLDGAGKTTILfKLKQDEFMQPI-PTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVIDS 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  99 SDEERMEETKEAMSEMLRHPRISGKPILVLANKQDKEGALGEADVIECLSLeklvneHKCLC----QIEPCSAISGYGkk 174
Cdd:cd04158  77 SHRDRVSEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEMTELLSL------HKLCCgrswYIQGCDARSGMG-- 148

                       170
                ....*....|..
gi 74355660 175 idksIKKGLYWL 186
Cdd:cd04158 149 ----LYEGLDWL 156
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 24-137 6.69e-14

small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model. [Unknown function, General]


Pssm-ID: 272973 [Multi-domain]  Cd Length: 162  Bit Score: 68.94  E-value: 6.69e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660    24 LLMVGLDNAGKTAT------AKGIQGEYPEDVAPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVD 97
Cdd:TIGR00231   4 IVIVGHPNVGKSTLlnsllgNKGSITEYYPGTTRNYVTTVIEEDGKTYKFNLLDTAGQEDYDAIRRLYYPQVERSLRVFD 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 74355660    98 -SSDEERMEETKEAMSEMLRHPRISGKPILVLANKQDKEGA 137
Cdd:TIGR00231  84 iVILVLDVEEILEKQTKEIIHHADSGVPIILVGNKIDLKDA 124
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
20-172 3.19e-13

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 67.70  E-value: 3.19e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  20 RKVTLLMVGLDNAGKTATAKGIQGEY--PEDVAPTVG----FSKINLRQGKFEVTIFDLGGGIRIRGIWKNY---YAESY 90
Cdd:COG1100   2 GEKKIVVVGTGGVGKTSLVNRLVGDIfsLEKYLSTNGvtidKKELKLDGLDVDLVIWDTPGQDEFRETRQFYarqLTGAS 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  91 GVIFVVDSSDEERMEETKEAMSEMLRHPRISgkPILVLANKQDKegaLGEADVIECLSLEKLVNEHKCLCQIePCSAISG 170
Cdd:COG1100  82 LYLFVVDGTREETLQSLYELLESLRRLGKKS--PIILVLNKIDL---YDEEEIEDEERLKEALSEDNIVEVV-ATSAKTG 155


                ..
gi 74355660 171 YG 172
Cdd:COG1100 156 EG 157
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 27-172 4.98e-13

Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions.


Pssm-ID: 206648 [Multi-domain]  Cd Length: 161  Bit Score: 66.71  E-value: 4.98e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  27 VGLDNAGKTAT----AKGIQGEYPEDVAPTVGFSKINLR--QGKFEVTIFDLGGGIRIRGIWKNYYAESY-----GVIFV 95
Cdd:cd00882   3 VGRGGVGKSSLlnalLGGEVGEVSDVPGTTRDPDVYVKEldKGKVKLVLVDTPGLDEFGGLGREELARLLlrgadLILLV 82

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 74355660  96 VDSSDEERMEETKEAMSEMLRHPrisGKPILVLANKQDKegaLGEADVIECLSLEKLVNEHKclCQIEPCSAISGYG 172
Cdd:cd00882  83 VDSTDRESEEDAKLLILRRLRKE---GIPIILVGNKIDL---LEEREVEELLRLEELAKILG--VPVFEVSAKTGEG 151
SR_beta cd04105
Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms ...
 23-133 7.53e-10

Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms the heterodimeric signal recognition particle (SRP); Signal recognition particle receptor, beta subunit (SR-beta). SR-beta and SR-alpha form the heterodimeric signal recognition particle (SRP or SR) receptor that binds SRP to regulate protein translocation across the ER membrane. Nascent polypeptide chains are synthesized with an N-terminal hydrophobic signal sequence that binds SRP54, a component of the SRP. SRP directs targeting of the ribosome-nascent chain complex (RNC) to the ER membrane via interaction with the SR, which is localized to the ER membrane. The RNC is then transferred to the protein-conducting channel, or translocon, which facilitates polypeptide translation across the ER membrane or integration into the ER membrane. SR-beta is found only in eukaryotes; it is believed to control the release of the signal sequence from SRP54 upon binding of the ribosome to the translocon. High expression of SR-beta has been observed in human colon cancer, suggesting it may play a role in the development of this type of cancer.


Pssm-ID: 206691 [Multi-domain]  Cd Length: 202  Bit Score: 58.49  E-value: 7.53e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  23 TLLMVGLDNAGKTAT-AKGIQGEYPEDVA---PTVGFSKINLRQGKFeVTIFDLGGGIRIR-GIWKNYYAESYGVIFVVD 97
Cdd:cd04105   2 TVLLLGPSDSGKTALfTKLTTGKVRSTVTsiePNVASFYSNSSKGKK-LTLVDVPGHEKLRdKLLEYLKASLKAIVFVVD 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 74355660  98 SSD-EERMEETKEAMSEML----RHPRisGKPILVLANKQD 133
Cdd:cd04105  81 SATfQKNIRDVAEFLYDILtdleKIKN--KIPILIACNKQD 119
RalA_RalB cd04139
Ral (Ras-like) family containing highly homologous RalA and RalB; The Ral (Ras-like) subfamily ...
 24-136 4.16e-08

Ral (Ras-like) family containing highly homologous RalA and RalB; The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (>80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exocyst and for localizing the exocyst to the leading edge of migrating cells. In human cancer cells, RalA is required to support anchorage-independent proliferation and RalB is required to suppress apoptosis. RalA has been shown to localize to the plasma membrane while RalB is localized to the intracellular vesicles. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206710 [Multi-domain]  Cd Length: 163  Bit Score: 52.43  E-value: 4.16e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  24 LLMVGLDNAGKTA-TAKGIQGEYPEDVAPTVGFS---KINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSS 99
Cdd:cd04139   3 VIMVGSGGVGKSAlTLQFMYDEFVEDYEPTKADSyrkKVVLDGEEVQLNILDTAGQEDYAAIRDNYFRSGEGFLLVFSIT 82

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 74355660 100 DEERMEETKEAMSEMLRHPRISGKPILVLANKQDKEG 136
Cdd:cd04139  83 DMESFTALAEFREQILRVKEDDNVPLLLVGNKCDLED 119
Rab cd00154
Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases ...
 24-172 1.89e-06

Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which mask C-terminal lipid binding and promote cytosolic localization. While most unicellular organisms possess 5-20 Rab members, several have been found to possess 60 or more Rabs; for many of these Rab isoforms, homologous proteins are not found in other organisms. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Since crystal structures often lack C-terminal residues, the lipid modification site is not available for annotation in many of the CDs in the hierarchy, but is included where possible.


Pssm-ID: 206640 [Multi-domain]  Cd Length: 159  Bit Score: 47.45  E-value: 1.89e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  24 LLMVGLDNAGKTATAKG-IQGEYPEDVAPTVG---FSK-INLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDS 98
Cdd:cd00154   3 IVLIGDSGVGKTSLLLRfVDNKFSENYKSTIGvdfKSKtIEVDGKKVKLQIWDTAGQERFRSITSSYYRGAHGAILVYDV 82

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 74355660  99 SDEERMEETKEAMSEMLRH--PRIsgkPILVLANKQDkegaLGEADVIECLSLEKLVNEHKCLCqIEpCSAISGYG 172
Cdd:cd00154  83 TNRESFENLDKWLNELKEYapPNI---PIILVGNKSD----LEDERQVSTEEAQQFAKENGLLF-FE-TSAKTGEN 149
Rab18 cd01863
Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic ...
 24-136 7.86e-06

Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206656 [Multi-domain]  Cd Length: 161  Bit Score: 45.76  E-value: 7.86e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  24 LLMVGLDNAGKTATAKG-IQGEYPEDVAPTVGF----SKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDS 98
Cdd:cd01863   3 ILLIGDSGVGKSSLLLRfTDDTFDEDLSSTIGVdfkvKTVTVDGKKVKLAIWDTAGQERFRTLTSSYYRGAQGVILVYDV 82

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 74355660  99 SDEERMEETKEAMSEMLRHPRISGKPILVLANKQDKEG 136
Cdd:cd01863  83 TRRDTFDNLDTWLNELDTYSTNPDAVKMLVGNKIDKEN 120
PLN03118 PLN03118
Rab family protein; Provisional
 24-167 9.93e-06

Rab family protein; Provisional


Pssm-ID: 215587 [Multi-domain]  Cd Length: 211  Bit Score: 46.20  E-value: 9.93e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660   24 LLMVGLDNAGKTATAKGIQGEYPEDVAPTVG--FSKINLRQG--KFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSS 99
Cdd:PLN03118  17 ILLIGDSGVGKSSLLVSFISSSVEDLAPTIGvdFKIKQLTVGgkRLKLTIWDTAGQERFRTLTSSYYRNAQGIILVYDVT 96

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 74355660  100 DEERMEETKEAMSEMLRHPRISGKPI-LVLANKQDKEgalGEADVI--ECLSLEKlvnEHKCLcqIEPCSA 167
Cdd:PLN03118  97 RRETFTNLSDVWGKEVELYSTNQDCVkMLVGNKVDRE---SERDVSreEGMALAK---EHGCL--FLECSA 159
Roc pfam08477
Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial ...
 24-133 3.05e-05

Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial Rho proteins (Miro-1, and Miro-2) and atypical Rho GTPases. Full-length proteins have a unique domain organization, with tandem GTP-binding domains and two EF hand domains (pfam00036) that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis.


Pssm-ID: 462490 [Multi-domain]  Cd Length: 114  Bit Score: 42.88  E-value: 3.05e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660    24 LLMVGLDNAGKTATAKG-IQGEYPEDVAPTVG-------FSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFV 95
Cdd:pfam08477   2 VVLLGDSGVGKTSLLKRfVDDTFDPKYKSTIGvdfktktVLENDDNGKKIKLNIWDTAGQERFRSLHPFYYRGAAAALLV 81

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 74355660    96 VDSSDEERMeetKEAMSEMLRHpriSGK-PILVLANKQD 133
Cdd:pfam08477  82 YDSRTFSNL---KYWLRELKKY---AGNsPVILVGNKID 114
Era_like cd00880
E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ...
 27-186 3.32e-05

E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngB), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. TrmE is ubiquitous in bacteria and is a widespread mitochondrial protein in eukaryotes, but is absent from archaea. The yeast member of TrmE family, MSS1, is involved in mitochondrial translation; bacterial members are often present in translation-related operons. FeoB represents an unusual adaptation of GTPases for high-affinity iron (II) transport. YihA (EngB) family of GTPases is typified by the E. coli YihA, which is an essential protein involved in cell division control. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. EngA and its orthologs are composed of two GTPase domains and, since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family.


Pssm-ID: 206646 [Multi-domain]  Cd Length: 161  Bit Score: 43.77  E-value: 3.32e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  27 VGLDNAGKTATAKGIQGEYPEDVAPTVGFSK-INLR----QGKFEVTIFDLGG----GIRIRGIWKNYY---AESYGVIF 94
Cdd:cd00880   3 FGRPNVGKSSLLNALLGQNVGIVSPIPGTTRdPVRKewelLPLGPVVLIDTPGldeeGGLGRERVEEARqvaDRADLVLL 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  95 VVDSS-DEERMEETKEAMSEMlrhprisGKPILVLANKQDKEGAlGEADVIECLSLEKLVNEHKCLcqiePCSAISgyGK 173
Cdd:cd00880  83 VVDSDlTPVEEEAKLGLLRER-------GKPVLLVLNKIDLVPE-SEEEELLRERKLELLPDLPVI----AVSALP--GE 148

                       170
                ....*....|...
gi 74355660 174 KIDKSIKKGLYWL 186
Cdd:cd00880 149 GIDELRKKIAELL 161
SRPRB pfam09439
Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition ...
 20-133 1.60e-04

Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase which anchors the alpha subunit to the endoplasmic reticulum membrane.


Pssm-ID: 462797 [Multi-domain]  Cd Length: 181  Bit Score: 42.43  E-value: 1.60e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660    20 RKVTLLMVGLDNAGKTAT-AKGIQGEYPEDVA---PTVGFsKINLRQGkFEVTIFDLGGGIRIRGIWKNYYAES---YGV 92
Cdd:pfam09439   2 SQPAVIIAGLCDSGKTSLfTLLTTDSVRPTVTsqePSAAY-RYMLNKG-NSFTLIDFPGHVKLRYKLLETLKDSsslKGI 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 74355660    93 IFVVDSS-DEERMEETKEAMSEML--RHPRISGKPILVLANKQD 133
Cdd:pfam09439  80 VFVVDSTiFPKEVTDTAEFLYDILsiTELLKNGIDILIACNKQE 123
PRK03003 PRK03003
GTP-binding protein Der; Reviewed
 92-149 3.17e-04

GTP-binding protein Der; Reviewed


Pssm-ID: 179525 [Multi-domain]  Cd Length: 472  Bit Score: 43.03  E-value: 3.17e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 74355660   92 VIFVVDSSdeERMEETKEAMSEMLRHpriSGKPILVLANKQDkeGALGEADVIECLSL 149
Cdd:PRK03003 121 VLFVVDAT--VGATATDEAVARVLRR---SGKPVILAANKVD--DERGEADAAALWSL 171
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
 24-172 4.21e-04

Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices.


Pssm-ID: 425451 [Multi-domain]  Cd Length: 162  Bit Score: 40.58  E-value: 4.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660    24 LLMVGLDNAGKTA-TAKGIQGEYPEDVAPTVGF----SKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDS 98
Cdd:pfam00071   2 LVLVGDGGVGKSSlLIRFTQNKFPEEYIPTIGVdfytKTIEVDGKTVKLQIWDTAGQERFRALRPLYYRGADGFLLVYDI 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 74355660    99 SDEERMEETKEAMSEMLRHPRiSGKPILVLANKQDkegaLGEADVIECLSLEKLVNEHKCLcQIEpCSAISGYG 172
Cdd:pfam00071  82 TSRDSFENVKKWVEEILRHAD-ENVPIVLVGNKCD----LEDQRVVSTEEGEALAKELGLP-FME-TSAKTNEN 148
RAB smart00175
Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.
 24-135 1.42e-03

Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.


Pssm-ID: 197555 [Multi-domain]  Cd Length: 164  Bit Score: 39.03  E-value: 1.42e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660     24 LLMVGLDNAGKTA-TAKGIQGEYPEDVAPTVG--F-SK-INLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDS 98
Cdd:smart00175   3 IILIGDSGVGKSSlLSRFTDGKFSEQYKSTIGvdFkTKtIEVDGKRVKLQIWDTAGQERFRSITSSYYRGAVGALLVYDI 82

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 74355660     99 SDEERMEETKEAMSEMLRH--PRIsgkPILVLANKQDKE 135
Cdd:smart00175  83 TNRESFENLENWLKELREYasPNV---VIMLVGNKSDLE 118
RJL cd04119
Rab GTPase family J-like (RabJ-like); RJLs are found in many protists and as chimeras with ...
 51-135 1.44e-03

Rab GTPase family J-like (RabJ-like); RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.


Pssm-ID: 133319 [Multi-domain]  Cd Length: 168  Bit Score: 39.26  E-value: 1.44e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  51 PTVGF----SKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSSDEERMEE----TKEAMSEMLRHPRISG 122
Cdd:cd04119  31 PTIGIdygvKKVSVRNKEVRVNFFDLSGHPEYLEVRNEFYKDTQGVLLVYDVTDRQSFEAldswLKEMKQEGGPHGNMEN 110

                        90
                ....*....|...
gi 74355660 123 KPILVLANKQDKE 135
Cdd:cd04119 111 IVVVVCANKIDLT 123
MMR_HSR1 pfam01926
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ...
 27-131 1.53e-03

50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete activity of the protein of interacting with the 50S ribosome and binding of both adenine and guanine nucleotides, with a preference for guanine nucleotide.


Pssm-ID: 460387 [Multi-domain]  Cd Length: 113  Bit Score: 37.98  E-value: 1.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660    27 VGLDNAGKT------ATAKGIQGEYPedvAPTVGFSKINLRQGKFEVTIFDLGGGIRI----RGIWKNYYA--ESYGVIF 94
Cdd:pfam01926   5 VGRPNVGKStlinalTGAKAIVSDYP---GTTRDPNEGRLELKGKQIILVDTPGLIEGasegEGLGRAFLAiiEADLILF 81

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 74355660    95 VVDSSDEErmeetKEAMSEMLRHPRISGKPILVLANK 131
Cdd:pfam01926  82 VVDSEEGI-----TPLDEELLELLRENKKPIILVLNK 113
Rab12 cd04120
Rab GTPase family 12 (Rab12); Rab12 was first identified in canine cells, where it was ...
 25-135 1.70e-03

Rab GTPase family 12 (Rab12); Rab12 was first identified in canine cells, where it was localized to the Golgi complex. The specific function of Rab12 remains unknown, and inconsistent results about its cellular localization have been reported. More recent studies have identified Rab12 associated with post-Golgi vesicles, or with other small vesicle-like structures but not with the Golgi complex. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 206699 [Multi-domain]  Cd Length: 202  Bit Score: 39.61  E-value: 1.70e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  25 LMVGLDNAGKTATAK-----GIQGEYPEDVAPTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSS 99
Cdd:cd04120   4 IIIGSRGVGKTSLMErftddTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQERFNSITSAYYRSAKGIILVYDIT 83

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 74355660 100 DEERMEETKEAMsEMLRHPRISGKPILVLANKQDKE 135
Cdd:cd04120  84 KKETFDDLPKWM-KMIDKYASEDAELLLVGNKLDCE 118
CCDC47 pfam07946
PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of ...
 199-241 2.70e-03

PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex, formed by CCDC47 and Asterix proteins, acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. CCDC47 is required to maintain the stability of Asterix. CCDC47 is associated with various membrane-associated processes and is component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis. It is also involved in the regulation of calcium ion homeostasis in the ER, being also required for proper protein degradation via the ERAD (ER-associated degradation) pathway.


Pssm-ID: 462322  Cd Length: 323  Bit Score: 39.47  E-value: 2.70e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 74355660   199 ERIQKETTEQRALEEQEKQERAERVRKLREERKQNEQEQAELD 241
Cdd:pfam07946 271 EKIKKAAEEERAEEAQEKKEEAKKKEREEKLAKLSPEEQRKYE 313
Rab33B_Rab33A cd04115
Rab GTPase family 33 includes Rab33A and Rab33B; Rab33B/Rab33A subfamily. Rab33B is ...
 20-133 3.05e-03

Rab GTPase family 33 includes Rab33A and Rab33B; Rab33B/Rab33A subfamily. Rab33B is ubiquitously expressed in mouse tissues and cells, where it is localized to the medial Golgi cisternae. It colocalizes with alpha-mannose II. Together with the other cisternal Rabs, Rab6A and Rab6A', it is believed to regulate the Golgi response to stress and is likely a molecular target in stress-activated signaling pathways. Rab33A (previously known as S10) is expressed primarily in the brain and immune system cells. In humans, it is located on the X chromosome at Xq26 and its expression is down-regulated in tuberculosis patients. Experimental evidence suggests that Rab33A is a novel CD8+ T cell factor that likely plays a role in tuberculosis disease processes. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133315 [Multi-domain]  Cd Length: 170  Bit Score: 38.19  E-value: 3.05e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  20 RKVTLLMVGLDNAGKTA-TAKGIQGEYPEDVAPTVG--FSK--INLRQGKFEVTIFDLGGGIRIR-GIWKNYYAESYGVI 93
Cdd:cd04115   1 RIFKIIVIGDSNVGKTClTYRFCAGRFPERTEATIGvdFRErtVEIDGERIKVQLWDTAGQERFRkSMVQHYYRNVHAVV 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 74355660  94 FVVDSSDEERMEETKEAMSEMLRHPRISGKPILVLANKQD 133
Cdd:cd04115  81 FVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCD 120
G-alpha pfam00503
G-protein alpha subunit; G proteins couple receptors of extracellular signals to intracellular ...
 51-133 4.38e-03

G-protein alpha subunit; G proteins couple receptors of extracellular signals to intracellular signaling pathways. The G protein alpha subunit binds guanyl nucleotide and is a weak GTPase. A set of residues that are unique to G-alpha as compared to its ancestor the Arf-like family form a ring of residues centered on the nucleotide binding site. A Ggamma is found fused to an inactive Galpha in the Dictyostelium protein gbqA.


Pssm-ID: 459835 [Multi-domain]  Cd Length: 316  Bit Score: 38.72  E-value: 4.38e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660    51 PTVGFSKINLRQGKFEVTIFDLGGGIRIRGIWKNYYAESYGVIFVVDSSD-----EE-----RMEETKEAMSEMLRHPRI 120
Cdd:pfam00503 153 KTTGIIETKFEFKGLKFRLFDVGGQRSERKKWIHCFEDVTAIIFVVSLSEydqvlYEddstnRMEESLKLFEEICNSPWF 232

                          90
                  ....*....|...
gi 74355660   121 SGKPILVLANKQD 133
Cdd:pfam00503 233 KNTPIILFLNKKD 245
EngA1 cd01894
EngA1 GTPase contains the first domain of EngA; This EngA1 subfamily CD represents the first ...
 92-172 4.50e-03

EngA1 GTPase contains the first domain of EngA; This EngA1 subfamily CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.


Pssm-ID: 206681 [Multi-domain]  Cd Length: 157  Bit Score: 37.41  E-value: 4.50e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74355660  92 VIFVVDSsDEERMEETKEaMSEMLRHpriSGKPILVLANKQDKEGALGEADVIECLSLEKLVnehkclcqiePCSAISGY 171
Cdd:cd01894  80 ILFVVDG-REGLTPADEE-IAKYLRK---SKKPVILVVNKIDNIKEEEEAAEFYSLGFGEPI----------PISAEHGR 144


                .
gi 74355660 172 G 172
Cdd:cd01894 145 G 145
rne PRK10811
ribonuclease E; Reviewed
 198-259 5.21e-03

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 39.25  E-value: 5.21e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 74355660   198 NERIQKETTEQ-RALEEQEKQERAERVRKLREERKQNEQEQAEL--DGTSGLAELDPEPTNPFQP 259
Cdd:PRK10811  654 RESQQAEVTEKaRTQDEQQQAPRRERQRRRNDEKRQAQQEAKALnvEEQSVQETEQEERVQQVQP 718
PRK09173 PRK09173
F0F1 ATP synthase subunit B; Validated
 190-240 9.77e-03

F0F1 ATP synthase subunit B; Validated


Pssm-ID: 169691 [Multi-domain]  Cd Length: 159  Bit Score: 36.64  E-value: 9.77e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 74355660  190 IARDFDALNERIQKETTEQRALEEQEKQERAERVRKlreeRKQNEQEQAEL 240
Cdd:PRK09173  27 IARSLDARADRIKNELAEARRLREEAQQLLAEYQRK----RKEAEKEAADI 73
 
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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