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Conserved domains on  [gi|1186517883|ref|NP_001337843|]
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cytoplasmic dynein 2 intermediate chain 1 isoform b [Homo sapiens]

Protein Classification

WD40 repeat domain-containing protein( domain architecture ID 1000017)

WD40 repeat domain-containing protein folds into a beta-propeller structure and functions as a scaffold, providing a platform for the interaction and assembly of several proteins into a signalosome; similar to a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly

CATH:  2.130.10.10
Gene Ontology:  GO:0005515
PubMed:  10322433|8090199|30069656|29026209
SCOP:  4002744

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PTZ00121 super family cl31754
MAEBL; Provisional
 5-289 8.79e-07

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 53.22  E-value: 8.79e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883    5 EHKEPRCRDPDQDARSRDRVAEVHTAKESPRGerDRDRQRERRRDAKDREKEKLKEKHREAEKSHSRGKDREKEKDRRAR 84
Cdd:PTZ00121  1493 EEAKKKADEAKKAAEAKKKADEAKKAEEAKKA--DEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAK 1570

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883   85 KEELRQTVAHH--NLLGQETRDR----QLLERAERKGRSVSKVRSEEKDEDSERGDEDRERRYRERKLQYGDSKDNPLKY 158
Cdd:PTZ00121  1571 KAEEDKNMALRkaEEAKKAEEARieevMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAE 1650

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  159 WLYKEEGERRHRKPREPDRDNKHREKSSTREKREKYSKEKSNSFSDKGEERHK----------EKRHKEGFHFDDERHQS 228
Cdd:PTZ00121  1651 ELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKaeelkkkeaeEKKKAEELKKAEEENKI 1730

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1186517883  229 NVDRKEKSAKDEPRKRES--QNGEHRNRGASSKRDGTSS-----QHAENLVRNHGKDKDSRRKHGHEE 289
Cdd:PTZ00121  1731 KAEEAKKEAEEDKKKAEEakKDEEEKKKIAHLKKEEEKKaeeirKEKEAVIEEELDEEDEKRRMEVDK 1798
WD40 super family cl29593
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 866-938 1.16e-03

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


The actual alignment was detected with superfamily member cd00200:

Pssm-ID: 475233 [Multi-domain]  Cd Length: 289  Bit Score: 41.94  E-value: 1.16e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1186517883  866 VNVIDFSPFGEPiFLAGCSDGSIRLHQLSSAFPLLQWDSSTDshAVTGLQWSPTRpAVFLVQDDTSNIYIWDL 938
Cdd:cd00200    180 VNSVAFSPDGEK-LLSSSSDGTIKLWDLSTGKCLGTLRGHEN--GVNSVAFSPDG-YLLASGSEDGTIRVWDL 248
 
Name Accession Description Interval E-value
PTZ00121 PTZ00121
MAEBL; Provisional
 5-289 8.79e-07

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 53.22  E-value: 8.79e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883    5 EHKEPRCRDPDQDARSRDRVAEVHTAKESPRGerDRDRQRERRRDAKDREKEKLKEKHREAEKSHSRGKDREKEKDRRAR 84
Cdd:PTZ00121  1493 EEAKKKADEAKKAAEAKKKADEAKKAEEAKKA--DEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAK 1570

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883   85 KEELRQTVAHH--NLLGQETRDR----QLLERAERKGRSVSKVRSEEKDEDSERGDEDRERRYRERKLQYGDSKDNPLKY 158
Cdd:PTZ00121  1571 KAEEDKNMALRkaEEAKKAEEARieevMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAE 1650

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  159 WLYKEEGERRHRKPREPDRDNKHREKSSTREKREKYSKEKSNSFSDKGEERHK----------EKRHKEGFHFDDERHQS 228
Cdd:PTZ00121  1651 ELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKaeelkkkeaeEKKKAEELKKAEEENKI 1730

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1186517883  229 NVDRKEKSAKDEPRKRES--QNGEHRNRGASSKRDGTSS-----QHAENLVRNHGKDKDSRRKHGHEE 289
Cdd:PTZ00121  1731 KAEEAKKEAEEDKKKAEEakKDEEEKKKIAHLKKEEEKKaeeirKEKEAVIEEELDEEDEKRRMEVDK 1798
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 51-202 7.73e-05

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 46.42  E-value: 7.73e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883   51 KDREKEKLKEKHREaekshsRGKDREKEKDRRARKEELRQTVAHHnllgqETRDRQLLERAERKGRSVSKVRSEEKDEDS 130
Cdd:TIGR01642    1 RDEEPDREREKSRG------RDRDRSSERPRRRSRDRSRFRDRHR-----RSRERSYREDSRPRDRRRYDSRSPRSLRYS 69

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1186517883  131 ERGDedrerryrerklqygdSKDNPlkywlykeegeRRHRKPREPDRDNKHREKSSTREKREKYSKEKSNSF 202
Cdd:TIGR01642   70 SVRR----------------SRDRP-----------RRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLW 114
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 54-254 3.19e-04

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 44.73  E-value: 3.19e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883   54 EKEKLK-EKHREAEKSHSRGKDREKEkdrRARKEELRQTVAHHNLLGQETRDRQLL-ERAERKGRSVSKVRSEEkdEDSE 131
Cdd:pfam17380  338 EQERMAmERERELERIRQEERKRELE---RIRQEEIAMEISRMRELERLQMERQQKnERVRQELEAARKVKILE--EERQ 412

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  132 RGDEDRERRYRERKLQYGDSKDNPLKYW----------LYKEEGERRHRKPR----EPDRDNKHREKSSTREKREKYSKE 197
Cdd:pfam17380  413 RKIQQQKVEMEQIRAEQEEARQREVRRLeeeraremerVRLEEQERQQQVERlrqqEEERKRKKLELEKEKRDRKRAEEQ 492

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1186517883  198 KSNSFSDKGEERHK----EKRHKEGFHFDDERHQSNVDRKEKSAKDEPRKRESQNGEHRNR 254
Cdd:pfam17380  493 RRKILEKELEERKQamieEERKRKLLEKEMEERQKAIYEEERRREAEEERRKQQEMEERRR 553
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 866-938 1.16e-03

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 41.94  E-value: 1.16e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1186517883  866 VNVIDFSPFGEPiFLAGCSDGSIRLHQLSSAFPLLQWDSSTDshAVTGLQWSPTRpAVFLVQDDTSNIYIWDL 938
Cdd:cd00200    180 VNSVAFSPDGEK-LLSSSSDGTIKLWDLSTGKCLGTLRGHEN--GVNSVAFSPDG-YLLASGSEDGTIRVWDL 248
 
Name Accession Description Interval E-value
PTZ00121 PTZ00121
MAEBL; Provisional
 5-289 8.79e-07

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 53.22  E-value: 8.79e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883    5 EHKEPRCRDPDQDARSRDRVAEVHTAKESPRGerDRDRQRERRRDAKDREKEKLKEKHREAEKSHSRGKDREKEKDRRAR 84
Cdd:PTZ00121  1493 EEAKKKADEAKKAAEAKKKADEAKKAEEAKKA--DEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAK 1570

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883   85 KEELRQTVAHH--NLLGQETRDR----QLLERAERKGRSVSKVRSEEKDEDSERGDEDRERRYRERKLQYGDSKDNPLKY 158
Cdd:PTZ00121  1571 KAEEDKNMALRkaEEAKKAEEARieevMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAE 1650

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  159 WLYKEEGERRHRKPREPDRDNKHREKSSTREKREKYSKEKSNSFSDKGEERHK----------EKRHKEGFHFDDERHQS 228
Cdd:PTZ00121  1651 ELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKaeelkkkeaeEKKKAEELKKAEEENKI 1730

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1186517883  229 NVDRKEKSAKDEPRKRES--QNGEHRNRGASSKRDGTSS-----QHAENLVRNHGKDKDSRRKHGHEE 289
Cdd:PTZ00121  1731 KAEEAKKEAEEDKKKAEEakKDEEEKKKIAHLKKEEEKKaeeirKEKEAVIEEELDEEDEKRRMEVDK 1798
PTZ00121 PTZ00121
MAEBL; Provisional
 5-403 5.50e-06

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 50.91  E-value: 5.50e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883    5 EHKEPRCRDPDQDARsrdRVAEVHTAKESPRGERDRDRQRERRRDAKDREKEKLK-EKHREAEKSHSRGKDREKEKDRRA 83
Cdd:PTZ00121  1114 ARKAEEAKKKAEDAR---KAEEARKAEDARKAEEARKAEDAKRVEIARKAEDARKaEEARKAEDAKKAEAARKAEEVRKA 1190

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883   84 ----RKEELRQTVAHHNllGQETRDRQLLERAE--RKGRSVSKVRSEEKDEDSERGDEDRERRYRERKLQYGDSKDNPLK 157
Cdd:PTZ00121  1191 eelrKAEDARKAEAARK--AEEERKAEEARKAEdaKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARR 1268

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  158 YWLYKEEgerrhrKPREPDRDNKHREKSSTREKREKYSKEKSNSFSDKGEERHKEKRHKEgfhfDDERHQSNVDRKEKSA 237
Cdd:PTZ00121  1269 QAAIKAE------EARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKK----KAEEAKKKADAAKKKA 1338

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  238 KDEPRKRESQNGEHRNRGASSKRDGTSSQHAENLVRNHGKDKDSRRKHGHEEGSSVwwKLDQRPGGEETVEIEKEETDLE 317
Cdd:PTZ00121  1339 EEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKAD--EAKKKAEEDKKKADELKKAAAA 1416

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  318 NARADAYTASCEDDFEDyeddfevcdgddDESSNEPESREKLEELplaqKKEIQEIQRAINA-----ENERIGELSLKLF 392
Cdd:PTZ00121  1417 KKKADEAKKKAEEKKKA------------DEAKKKAEEAKKADEA----KKKAEEAKKAEEAkkkaeEAKKADEAKKKAE 1480

                          410
                   ....*....|.
gi 1186517883  393 QKRGRTEFEKE 403
Cdd:PTZ00121  1481 EAKKADEAKKK 1491
PTZ00121 PTZ00121
MAEBL; Provisional
 21-279 4.82e-05

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 47.83  E-value: 4.82e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883   21 RDRVAEVHTAKESPRGERDRDRQRERRRDAKDREK-EKLKEKHREAEKS--HSRGKDREKEKDRRARK-EELRQtvAHHN 96
Cdd:PTZ00121  1450 KKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKaDEAKKKAEEAKKKadEAKKAAEAKKKADEAKKaEEAKK--ADEA 1527

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883   97 LLGQETRDRQLLERAE--RKGRSVSKV----RSEEKDEDSERGDEDRERRYRERKLQYGDSKDNPLKYWLYKEEGERRHR 170
Cdd:PTZ00121  1528 KKAEEAKKADEAKKAEekKKADELKKAeelkKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKM 1607

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  171 KPREPDRDNKHREKSSTREKREKySKEKSNSFSDKGEErhkEKRHKEGFHFDDERHQSNVDRKEKSAKDEPRKRES---Q 247
Cdd:PTZ00121  1608 KAEEAKKAEEAKIKAEELKKAEE-EKKKVEQLKKKEAE---EKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEakkA 1683

                          250       260       270
                   ....*....|....*....|....*....|..
gi 1186517883  248 NGEHRNRGASSKRDGTSSQHAENLVRNHGKDK 279
Cdd:PTZ00121  1684 EEDEKKAAEALKKEAEEAKKAEELKKKEAEEK 1715
PTZ00121 PTZ00121
MAEBL; Provisional
 2-407 5.80e-05

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 47.44  E-value: 5.80e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883    2 DLPEHKEPRCRDPDQDARSRDRVAEVHTAKESPRGERDRDRQRERRRDAKDREKEKLKEKHREAEKShsrgKDREKEKDR 81
Cdd:PTZ00121  1282 ELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAA----KAEAEAAAD 1357

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883   82 RARKEELRQTVAHHnllgQETRDRQLLERAERKGRSVSKVRSEEK--DEDSERGDEDRERRYRERKLQYGDSKDNPLKyw 159
Cdd:PTZ00121  1358 EAEAAEEKAEAAEK----KKEEAKKKADAAKKKAEEKKKADEAKKkaEEDKKKADELKKAAAAKKKADEAKKKAEEKK-- 1431

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  160 lYKEEGERRHRKPREPDRDNKHREKSSTREKREKYSKE--KSNSFSDKGEERHK-----------EKRHKEGFHFDDERH 226
Cdd:PTZ00121  1432 -KADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEakKADEAKKKAEEAKKadeakkkaeeaKKKADEAKKAAEAKK 1510

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  227 QSNVDRK--EKSAKDEPRKRESQNGEHRNRGASSKRDGTSSQHAENLVRNHGKDKDSRRKHGHEEGSSVWWKLDQRPGGE 304
Cdd:PTZ00121  1511 KADEAKKaeEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAE 1590

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  305 ETVEIEKEETDLENARADAYTASCEDDFEDYEddfevcdgddDESSNEPESREKLEELPLAQKKEIQEIQRAINAENE-- 382
Cdd:PTZ00121  1591 EARIEEVMKLYEEEKKMKAEEAKKAEEAKIKA----------EELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEEnk 1660

                          410       420
                   ....*....|....*....|....*.
gi 1186517883  383 -RIGELSLKLFQKRGRTEFEKEPRTD 407
Cdd:PTZ00121  1661 iKAAEEAKKAEEDKKKAEEAKKAEED 1686
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 51-202 7.73e-05

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 46.42  E-value: 7.73e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883   51 KDREKEKLKEKHREaekshsRGKDREKEKDRRARKEELRQTVAHHnllgqETRDRQLLERAERKGRSVSKVRSEEKDEDS 130
Cdd:TIGR01642    1 RDEEPDREREKSRG------RDRDRSSERPRRRSRDRSRFRDRHR-----RSRERSYREDSRPRDRRRYDSRSPRSLRYS 69

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1186517883  131 ERGDedrerryrerklqygdSKDNPlkywlykeegeRRHRKPREPDRDNKHREKSSTREKREKYSKEKSNSF 202
Cdd:TIGR01642   70 SVRR----------------SRDRP-----------RRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLW 114
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 54-254 3.19e-04

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 44.73  E-value: 3.19e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883   54 EKEKLK-EKHREAEKSHSRGKDREKEkdrRARKEELRQTVAHHNLLGQETRDRQLL-ERAERKGRSVSKVRSEEkdEDSE 131
Cdd:pfam17380  338 EQERMAmERERELERIRQEERKRELE---RIRQEEIAMEISRMRELERLQMERQQKnERVRQELEAARKVKILE--EERQ 412

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  132 RGDEDRERRYRERKLQYGDSKDNPLKYW----------LYKEEGERRHRKPR----EPDRDNKHREKSSTREKREKYSKE 197
Cdd:pfam17380  413 RKIQQQKVEMEQIRAEQEEARQREVRRLeeeraremerVRLEEQERQQQVERlrqqEEERKRKKLELEKEKRDRKRAEEQ 492

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1186517883  198 KSNSFSDKGEERHK----EKRHKEGFHFDDERHQSNVDRKEKSAKDEPRKRESQNGEHRNR 254
Cdd:pfam17380  493 RRKILEKELEERKQamieEERKRKLLEKEMEERQKAIYEEERRREAEEERRKQQEMEERRR 553
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 171-260 3.59e-04

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 44.50  E-value: 3.59e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  171 KPREPDRDN-----KHREKSSTREKREKYSKEKSNSFSDKGEER--HKEKRHKEGFHFDDERHQSNVDRKEKSAKDEPRK 243
Cdd:TIGR01642    1 RDEEPDREReksrgRDRDRSSERPRRRSRDRSRFRDRHRRSRERsyREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRR 80

                           90       100
                   ....*....|....*....|
gi 1186517883  244 RE---SQNGEHRNRGASSKR 260
Cdd:TIGR01642   81 RSrsvRSIEQHRRRLRDRSP 100
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 161-280 7.34e-04

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 43.37  E-value: 7.34e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  161 YKEEGERRHRKPREPDRDNKHREKSSTREKREKYSKEKSnsfSDKGEERHKEKrhkegfhfDDERhqsnvDRKEKSAKDE 240
Cdd:TIGR01622    2 YRDRERERLRDSSSAGDRDRRRDKGRERSRDRSRDRERS---RSRRRDRHRDR--------DYYR-----GRERRSRSRR 65

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1186517883  241 PRKRESQNGEHRNRGASSKRDGTSSQHAENLVRNHGKDKD 280
Cdd:TIGR01622   66 PNRRYRPREKRRRRGDSYRRRRDDRRSRREKPRARDGTPE 105
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 59-216 8.19e-04

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 43.34  E-value: 8.19e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883   59 KEKHREAEKSHSRGKDREKEKDRRARKEELRQtvahhnllgqETRDRQLLERAERKG-RSVSKVRSEEKDEDSERgdedr 137
Cdd:TIGR01642    3 EEPDREREKSRGRDRDRSSERPRRRSRDRSRF----------RDRHRRSRERSYREDsRPRDRRRYDSRSPRSLR----- 67

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1186517883  138 erryrerklqygdskdnplkywlykeegERRHRKPREPDRdnkHREKSSTREKREkysKEKSNSFSDKGEERHKEKRHK 216
Cdd:TIGR01642   68 ----------------------------YSSVRRSRDRPR---RRSRSVRSIEQH---RRRLRDRSPSNQWRKDDKKRS 112
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 866-938 1.16e-03

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 41.94  E-value: 1.16e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1186517883  866 VNVIDFSPFGEPiFLAGCSDGSIRLHQLSSAFPLLQWDSSTDshAVTGLQWSPTRpAVFLVQDDTSNIYIWDL 938
Cdd:cd00200    180 VNSVAFSPDGEK-LLSSSSDGTIKLWDLSTGKCLGTLRGHEN--GVNSVAFSPDG-YLLASGSEDGTIRVWDL 248
Caldesmon pfam02029
Caldesmon;
13-271 2.62e-03

Caldesmon;


Pssm-ID: 460421 [Multi-domain]  Cd Length: 495  Bit Score: 41.39  E-value: 2.62e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883   13 DPDQDARSRDRVAevhtAKESPRGERDRDRQRERRRDAKDREKEKLKEKHREAEKSHSRGKDREKEKDRRARKEELRQTV 92
Cdd:pfam02029    3 DEEEAARERRRRA----REERRRQKEEEEPSGQVTESVEPNEHNSYEEDSELKPSGQGGLDEEEAFLDRTAKREERRQKR 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883   93 AHHNLLGQETRDRQLLER----AERKGR----SVSKVRSEEKDEDSERGDEDRERRYRERKLQYGDSKDNPLKYwlyKEE 164
Cdd:pfam02029   79 LQEALERQKEFDPTIADEkesvAERKENneeeENSSWEKEEKRDSRLGRYKEEETEIREKEYQENKWSTEVRQA---EEE 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  165 GERRHRKPRE----PDRDNKHREKSSTREKREKYSKEKSNSFSDKGEERHKEK------RHKEGFHFDDERHQSNVDRKE 234
Cdd:pfam02029  156 GEEEEDKSEEaeevPTENFAKEEVKDEKIKKEKKVKYESKVFLDQKRGHPEVKsqngeeEVTKLKVTTKRRQGGLSQSQE 235

                          250       260       270
                   ....*....|....*....|....*....|....*..
gi 1186517883  235 KSAKDEPRKRESQNGEHRNRgassKRDGTSSQHAENL 271
Cdd:pfam02029  236 REEEAEVFLEAEQKLEELRR----RRQEKESEEFEKL 268
PTZ00121 PTZ00121
MAEBL; Provisional
 53-403 6.40e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 40.51  E-value: 6.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883   53 REKEKLKEKHREAEKSHSRGKDREKEKDRRARKEELRQTVAHHNLLGQETRDRQLLERAE--RKGRSVSKVRSEEKDEDS 130
Cdd:PTZ00121  1084 KEDNRADEATEEAFGKAEEAKKTETGKAEEARKAEEAKKKAEDARKAEEARKAEDARKAEeaRKAEDAKRVEIARKAEDA 1163

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  131 ERGDEDRERRYRERKLQYGDSKDNPLKYWLYKEEGERRHRKPREPDRDNKHREKSSTREKREKYSKEKSNSFSDKGEE-- 208
Cdd:PTZ00121  1164 RKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEak 1243

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  209 RHKEKRHKEGFHFDDE-------RHQSNVDRKEKSAKDEPRK-------RESQNGEHRNRGASSKRDGTSSQHAENLVRN 274
Cdd:PTZ00121  1244 KAEEERNNEEIRKFEEarmahfaRRQAAIKAEEARKADELKKaeekkkaDEAKKAEEKKKADEAKKKAEEAKKADEAKKK 1323

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  275 --HGKDKDSRRKHGHEEGSsvwwKLDQRPGGEETVEIEKEETDLENARADAYTASCEDDFEDYEDDFEvcdgddDESSNE 352
Cdd:PTZ00121  1324 aeEAKKKADAAKKKAEEAK----KAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKA------EEKKKA 1393

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1186517883  353 PESREKLEElplaQKKEIQEIQRAiNAENERIGELSLKLFQKRGRTEFEKE 403
Cdd:PTZ00121  1394 DEAKKKAEE----DKKKADELKKA-AAAKKKADEAKKKAEEKKKADEAKKK 1439
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 51-219 8.18e-03

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 39.90  E-value: 8.18e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883   51 KDREKEKLKEKHREAEKSHSRGKDREKEKDRRARKEELRQTVAHHNLLGQETRDRqllERAERKGRSVSKVRSEEKDEDs 130
Cdd:TIGR01622    3 RDRERERLRDSSSAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRDRDYYRGR---ERRSRSRRPNRRYRPREKRRR- 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1186517883  131 ergdedrerryrerklqygdskdnplkywlyKEEGERRHRKPREPdRDNKHREKSSTREKREKYSKEKSNSFSDKGEERH 210
Cdd:TIGR01622   79 -------------------------------RGDSYRRRRDDRRS-RREKPRARDGTPEPLTEDERDRRTVFVQQLAARA 126


                   ....*....
gi 1186517883  211 KEKRHKEGF 219
Cdd:TIGR01622  127 RERDLYEFF 135
 
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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