RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15995
(683 letters)
>gnl|CDD|238121 cd00200, WD40, 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.
Length = 289
Score = 175 bits (445), Expect = 8e-50
Identities = 81/279 (29%), Positives = 137/279 (49%), Gaps = 15/279 (5%)
Query: 155 YIASGDISGKVRIWDTVNKEHILKNEFHPIGGPIKDIAWSPDNQRMVVVGEGRERFGHVF 214
+A+G G +++WD E + + H GP++D+A S D + ++ ++
Sbjct: 23 LLATGSGDGTIKVWDLETGELLRTLKGHT--GPVRDVAASADGTYLASGSS--DKTIRLW 78
Query: 215 MSETGTSVGEISGQSKPINSCDFKPSRPFRIITGSEDNTIAVFEGPPFKFKMTKQEHSRF 274
ETG V ++G + ++S F P + + S D TI V++ K T + H+ +
Sbjct: 79 DLETGECVRTLTGHTSYVSSVAFSPDGRI-LSSSSRDKTIKVWDVETGKCLTTLRGHTDW 137
Query: 275 VQAVRYSPSGSHFASAGFDGKVFLYDGASADLVSELGNPAHKGGVYAVAWKPDGTQLLTA 334
V +V +SP G+ AS+ DG + L+D + V+ L H G V +VA+ PDG +LL++
Sbjct: 138 VNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATL--TGHTGEVNSVAFSPDGEKLLSS 195
Query: 335 SGDKTCKLWDIETKSVVSEFIMGNQVEDQQVSCLW---QGDYLLTVSLSGFISYLDVNNP 391
S D T KLWD+ T + + + V+ + G L + S G I D+
Sbjct: 196 SSDGTIKLWDLSTGKCLGTL----RGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTG 251
Query: 392 STPIRVIKGHNKPITALALSPDRGTVFTGSHDGFITRWN 430
++ + GH +T+LA SPD + +GS DG I W+
Sbjct: 252 E-CVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 146 bits (371), Expect = 2e-39
Identities = 72/258 (27%), Positives = 115/258 (44%), Gaps = 12/258 (4%)
Query: 221 SVGEISGQSKPINSCDFKPSRPFRIITGSEDNTIAVFEGPPFKFKMTKQEHSRFVQAVRY 280
+ G + + F P + TGS D TI V++ + T + H+ V+ V
Sbjct: 1 LRRTLKGHTGGVTCVAFSPDGKL-LATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAA 59
Query: 281 SPSGSHFASAGFDGKVFLYDGASADLVSELGNPAHKGGVYAVAWKPDGTQLLTASGDKTC 340
S G++ AS D + L+D + + V L H V +VA+ PDG L ++S DKT
Sbjct: 60 SADGTYLASGSSDKTIRLWDLETGECVRTLT--GHTSYVSSVAFSPDGRILSSSSRDKTI 117
Query: 341 KLWDIETKSVVSEFIMGNQVEDQQVSCLWQGD--YLLTVSLSGFISYLDVNNPSTPIRVI 398
K+WD+ET ++ D S + D ++ + S G I D+ + +
Sbjct: 118 KVWDVETGKCLTTL---RGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGK-CVATL 173
Query: 399 KGHNKPITALALSPDRGTVFTGSHDGFITRWNAKTGENDRVQGAGHGNQINGMKA--TGE 456
GH + ++A SPD + + S DG I W+ TG+ GH N +N + G
Sbjct: 174 TGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLG-TLRGHENGVNSVAFSPDGY 232
Query: 457 LLYTCGIDDTIKQVDLSS 474
LL + D TI+ DL +
Sbjct: 233 LLASGSEDGTIRVWDLRT 250
Score = 140 bits (355), Expect = 3e-37
Identities = 79/329 (24%), Positives = 129/329 (39%), Gaps = 54/329 (16%)
Query: 315 HKGGVYAVAWKPDGTQLLTASGDKTCKLWDIETKSVVSEFIMGNQVEDQQVSCLWQGDYL 374
H GGV VA+ PDG L T SGD T K+WD+ET ++ G+ + V+ G YL
Sbjct: 8 HTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTL-KGHTGPVRDVAASADGTYL 66
Query: 375 LTVSLSGFISYLDVNNPSTPIRVIKGHNKPITALALSPDRGTVFTGSHDGFITRWNAKTG 434
+ S I D+ +R + GH ++++A SPD + + S D I W+ +TG
Sbjct: 67 ASGSSDKTIRLWDLETGE-CVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETG 125
Query: 435 ENDRVQGAGHGNQINGMKA--TGELLYTCGIDDTIKQVDLSSNAYSGPEVKLGSQPRGLD 492
+ GH + +N + G + + D TIK DL +
Sbjct: 126 KCLTTLR-GHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTG----------------- 167
Query: 493 IDENTLVTVTVKQISIVENGAKVSSLPIDYEPSSISLDHEHGLVAVGGADSKVHIYELNN 552
V ++ +S++ + + +D + +++L+
Sbjct: 168 --------KCVATLTGHTGEV-----------NSVAFSPDGEKLLSSSSDGTIKLWDLST 208
Query: 553 KSLSPKAELD-HLGPVTDCSFSPSNEYLVASDAHRKVVLYRV----PDFELAHNKEWGFH 607
L H V +FSP L + + ++ + L+ H
Sbjct: 209 GKC--LGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSG------H 260
Query: 608 SAKVNCVAWSPDSALVASGSLDTTIIIWS 636
+ V +AWSPD +ASGS D TI IW
Sbjct: 261 TNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 135 bits (342), Expect = 2e-35
Identities = 66/292 (22%), Positives = 117/292 (40%), Gaps = 27/292 (9%)
Query: 57 KNFLYTNG--NSVIIRNIENPAISDIYTEHSCAVNVAKYSPSGFYIASGDISGKVRIWDT 114
L T ++ + ++E + H+ V S G Y+ASG +R+WD
Sbjct: 21 GKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDL 80
Query: 115 VNKE--HILKNEFHPIGGPIKDIGTLLSLTSIRNILVLSIGFYIASGDISGKVRIWDTVN 172
E L + S+ + G ++S +++WD
Sbjct: 81 ETGECVRTLTGHTSYV----------SSVAFSPD------GRILSSSSRDKTIKVWDVET 124
Query: 173 KEHILKNEFHPIGGPIKDIAWSPDNQRMVVVGEGRERFGHVFMSETGTSVGEISGQSKPI 232
+ + +A+SPD V ++ ++ TG V ++G + +
Sbjct: 125 GK--CLTTLRGHTDWVNSVAFSPDGT--FVASSSQDGTIKLWDLRTGKCVATLTGHTGEV 180
Query: 233 NSCDFKPSRPFRIITGSEDNTIAVFEGPPFKFKMTKQEHSRFVQAVRYSPSGSHFASAGF 292
NS F P ++++ S D TI +++ K T + H V +V +SP G AS
Sbjct: 181 NSVAFSPDG-EKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSE 239
Query: 293 DGKVFLYDGASADLVSELGNPAHKGGVYAVAWKPDGTQLLTASGDKTCKLWD 344
DG + ++D + + V L H V ++AW PDG +L + S D T ++WD
Sbjct: 240 DGTIRVWDLRTGECVQTL--SGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 120 bits (302), Expect = 4e-30
Identities = 64/290 (22%), Positives = 114/290 (39%), Gaps = 45/290 (15%)
Query: 394 PIRVIKGHNKPITALALSPDRGTVFTGSHDGFITRWNAKTGENDRVQGAGHGNQINGMK- 452
R +KGH +T +A SPD + TGS DG I W+ +TGE R GH + +
Sbjct: 1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLR-TLKGHTGPVRDVAA 59
Query: 453 -ATGELLYTCGIDDTIKQVDLSSNAYSGPEVKLGSQPRGLDIDENTLVTVTVKQISIVEN 511
A G L + D TI+ DL + + T+T +
Sbjct: 60 SADGTYLASGSSDKTIRLWDLETG--------------------ECVRTLTGHTSYV--- 96
Query: 512 GAKVSSLPIDYEPSSISLDHEHGLVAVGGADSKVHIYELNNKSLSPKAELDHLGPVTDCS 571
SS++ + +++ D + ++++ H V +
Sbjct: 97 -------------SSVAFSPDGRILSSSSRDKTIKVWDVETGKCL-TTLRGHTDWVNSVA 142
Query: 572 FSPSNEYLVASDAHRKVVLYRVPDFELAHNKEWGFHSAKVNCVAWSPDSALVASGSLDTT 631
FSP ++ +S + L+ + + H+ +VN VA+SPD + S S D T
Sbjct: 143 FSPDGTFVASSSQDGTIKLWDLRTGKCVATLT--GHTGEVNSVAFSPDGEKLLSSSSDGT 200
Query: 632 IIIWSLASPAKHIIIKNAHPQSQITRLQWL-DNDLLVSVGQDCNTKIWEI 680
I +W L++ ++ H + + + D LL S +D ++W++
Sbjct: 201 IKLWDLSTGKCLGTLR-GHENG-VNSVAFSPDGYLLASGSEDGTIRVWDL 248
Score = 74.3 bits (183), Expect = 2e-14
Identities = 34/122 (27%), Positives = 54/122 (44%), Gaps = 5/122 (4%)
Query: 563 HLGPVTDCSFSPSNEYLVASDAHRKVVLYRVPDFELAHNKEWGFHSAKVNCVAWSPDSAL 622
H G VT +FSP + L + ++ + EL G H+ V VA S D
Sbjct: 8 HTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLR-TLKG-HTGPVRDVAASADGTY 65
Query: 623 VASGSLDTTIIIWSLASPAKHIIIKNAHPQSQITRLQWL-DNDLLVSVGQDCNTKIWEIA 681
+ASGS D TI +W L + + H S ++ + + D +L S +D K+W++
Sbjct: 66 LASGSSDKTIRLWDLETGECVRTLT-GH-TSYVSSVAFSPDGRILSSSSRDKTIKVWDVE 123
Query: 682 PF 683
Sbjct: 124 TG 125
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 138 bits (347), Expect = 7e-35
Identities = 102/435 (23%), Positives = 188/435 (43%), Gaps = 19/435 (4%)
Query: 47 PIVLGGDPKGKNFLYTNGNSVIIRNIENPAISDIYTEHSCAVNVAKYSPSGFYIASGDIS 106
++ G + L + ++ + S + H ++ +SP G + SG
Sbjct: 29 SLLSLGSSESGILLLALLSDSLVSLPD--LSSLLLRGHEDSITSIAFSPDGELLLSGSSD 86
Query: 107 GKVRIWDTVNKEHILKNEFHPIGGPIKDIGTLLSLTSIRNILVLSIGFYIASGDISGKVR 166
G +++WD N E ++K+ + + LS +IL+ AS + G V+
Sbjct: 87 GTIKLWDLDNGEKLIKSLEGLHDSSVSKL--ALSSPDGNSILL-------ASSSLDGTVK 137
Query: 167 IWDTVNKEHILKNEFHPIGGPIKDIAWSPDNQRMVVVGEGRERFGHVFMSETGTSVGEIS 226
+WD ++ L + +A+SPD +++ G + ++ TG + ++
Sbjct: 138 LWD-LSTPGKLIRTLEGHSESVTSLAFSPDG-KLLASGSSLDGTIKLWDLRTGKPLSTLA 195
Query: 227 GQSKPINSCDFKPSRPFRIITGSEDNTIAVFEGPPFKFKMTKQEHSRFVQAVRYSPSGSH 286
G + P++S F P I +GS D TI +++ K + +SP GS
Sbjct: 196 GHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSSFSPDGSL 255
Query: 287 FASAGFDGKVFLYDGASADLVSELGNPAHKGGVYAVAWKPDGTQLLTASGDKTCKLWDIE 346
AS DG + L+D + H V +VA+ PDG L + S D T +LWD+E
Sbjct: 256 LASGSSDGTIRLWD-LRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLE 314
Query: 347 TKSVVSEF-IMGNQVEDQQVSCLWQGDYLLTVSLSGFISYLDVNNPSTPIRVIKGHNKPI 405
T ++S + G++ +S G L++ L P++ ++GH+ +
Sbjct: 315 TGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTLEGHS-NV 373
Query: 406 TALALSPDRGTVFTGSHDGFITRWNAKTGENDRVQGAGHGNQINGMK--ATGELLYTCGI 463
+++ SPD V +GS DG + W+ TG R GH +++ + G+ L +
Sbjct: 374 LSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLD-GHTSRVTSLDFSPDGKSLASGSS 432
Query: 464 DDTIKQVDLSSNAYS 478
D+TI+ DL ++ S
Sbjct: 433 DNTIRLWDLKTSLKS 447
Score = 129 bits (323), Expect = 7e-32
Identities = 109/429 (25%), Positives = 184/429 (42%), Gaps = 50/429 (11%)
Query: 261 PFKFKMTKQEHSRFVQAVRYSPSGSHFASAGFDGKVFLYDGASADLVSELGNPAHKGGVY 320
P + + H + ++ +SP G S DG + L+D + + + + H V
Sbjct: 54 PDLSSLLLRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVS 113
Query: 321 AVAWK-PDGTQLLTASG--DKTCKLWDIETKSVVSEFIMGNQVEDQQVSCLWQGDYLLTV 377
+A PDG +L AS D T KLWD+ T + + G+ ++ G L +
Sbjct: 114 KLALSSPDGNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASG 173
Query: 378 S-LSGFISYLDVNNPSTPIRVIKGHNKPITALALSPDRGTVF-TGSHDGFITRWNAKTGE 435
S L G I D+ P+ + GH P+++LA SPD G + +GS DG I W+ TG+
Sbjct: 174 SSLDGTIKLWDLRT-GKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGK 232
Query: 436 NDRVQGAGH-GNQINGMKATGELLYTCGIDDTIKQVDLSSNAYSGPEVKLGSQPRGLDID 494
R +GH + ++ G LL + D TI+ DL S
Sbjct: 233 LLRSTLSGHSDSVVSSFSPDGSLLASGSSDGTIRLWDLRS-------------------S 273
Query: 495 ENTLVTVTVKQISIVENGAKVSSLPIDYEPSSISLDHEHGLVAVGGADSKVHIYELNNKS 554
+ L T++ S+ S++ + L+A G +D V +++L
Sbjct: 274 SSLLRTLSGHSSSV----------------LSVAFSPDGKLLASGSSDGTVRLWDLETGK 317
Query: 555 L-SPKAELDHLGPVTDCSFSPSNEYLVASDAHRK-VVLYRVPDFELAHNKEWGFHSAKVN 612
L S H GPV+ SFSP LV+ + + L+ + + E + V
Sbjct: 318 LLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTLE---GHSNVL 374
Query: 613 CVAWSPDSALVASGSLDTTIIIWSLASPAKHIIIKNAHPQSQITRLQWL-DNDLLVSVGQ 671
V++SPD +V+SGS D T+ +W L++ + ++ S++T L + D L S
Sbjct: 375 SVSFSPDGRVVSSGSTDGTVRLWDLSTGS--LLRNLDGHTSRVTSLDFSPDGKSLASGSS 432
Query: 672 DCNTKIWEI 680
D ++W++
Sbjct: 433 DNTIRLWDL 441
Score = 118 bits (295), Expect = 3e-28
Identities = 102/496 (20%), Positives = 189/496 (38%), Gaps = 77/496 (15%)
Query: 156 IASGDISGKVRIWDTVNKEHILKN-------EFHPIGGPIKDIAWSPDNQRMVVVGEGRE 208
S + I L + I IA+SPD + ++ +
Sbjct: 29 SLLSLGSSESGILLLALLSDSLVSLPDLSSLLLRGHEDSITSIAFSPDGELLLS--GSSD 86
Query: 209 RFGHVFMSETGTSVGEI--SGQSKPINSCDFK-PSRPFRIITGSE-DNTIAVFE-GPPFK 263
++ + G + + ++ P ++ S D T+ +++ P K
Sbjct: 87 GTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDGNSILLASSSLDGTVKLWDLSTPGK 146
Query: 264 FKMTKQEHSRFVQAVRYSPSGSHFASAG-FDGKVFLYDGASADLVSELGNPAHKGGVYAV 322
T + HS V ++ +SP G AS DG + L+D + +S L H V ++
Sbjct: 147 LIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAG--HTDPVSSL 204
Query: 323 AWKPDGT-QLLTASGDKTCKLWDIETKSVVSEFIMGNQVEDQQVSCL-WQGDYLLTVSLS 380
A+ PDG + + S D T +LWD+ T ++ + G+ D VS G L + S
Sbjct: 205 AFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHS--DSVVSSFSPDGSLLASGSSD 262
Query: 381 GFISYLDVNNPSTPIRVIKGHNKPITALALSPDRGTVFTGSHDGFITRWNAKTGEN-DRV 439
G I D+ + S+ +R + GH+ + ++A SPD + +GS DG + W+ +TG+ +
Sbjct: 263 GTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSL 322
Query: 440 QGAGHGNQINGMKATGE---LLYTCGIDDTIKQVDLSSNAYSGPEVKLGSQPRGLDIDEN 496
GH ++ + + + L+ D TI+ DL +
Sbjct: 323 TLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTG--------------------- 361
Query: 497 TLVTVTVKQISIVENGAKVSSLPIDYEPSSISLDHEHGLVAVGGADSKVHIYELNNKSLS 556
+ + L + + P +V+ G D V +++L+ SL
Sbjct: 362 ---------KPLKTLEGHSNVLSVSFSPDGR-------VVSSGSTDGTVRLWDLSTGSLL 405
Query: 557 PKAELDHLGPVTDCSFSPSNEYLVASDAHRKVVLYRVPDFELAHNKEWGFHSAKVNCVAW 616
H VT FSP + L + + + L+ + + V++
Sbjct: 406 RN-LDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDLKT--------------SLKSVSF 450
Query: 617 SPDSALVASGSLDTTI 632
SPD ++AS S D ++
Sbjct: 451 SPDGKVLASKSSDLSV 466
Score = 80.5 bits (197), Expect = 6e-16
Identities = 69/318 (21%), Positives = 125/318 (39%), Gaps = 39/318 (12%)
Query: 22 KGKNFLYTNGNKYIFATLPRTQRGQPIVLGGDPKGKNFLYTNGNSVIIRNIENPAISDIY 81
GK G+ ++L + G ++ G G L+ ++R+
Sbjct: 187 TGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRST--------L 238
Query: 82 TEHSCAVNVAKYSPSGFYIASGDISGKVRIWDTVNKEHILKNEFHPIGGPIKDIGTLLSL 141
+ HS V+ +SP G +ASG G +R+WD + +L+
Sbjct: 239 SGHS-DSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRT-------------LSGHS 284
Query: 142 TSIRNILVLSIGFYIASGDISGKVRIWDTVNKEHILKNEFHPIGGPIKDIAWSPDNQRMV 201
+S+ ++ G +ASG G VR+WD + + GP+ +++SPD +
Sbjct: 285 SSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSL-L 343
Query: 202 VVGEGRERFGHVFMSETGTSVGEISGQSKPINSCDFKPSRPFRIITGSEDNTIAVFEGPP 261
V G + ++ TG + + G S + S F P + +GS D T+ +++
Sbjct: 344 VSGGSDDGTIRLWDLRTGKPLKTLEGHS-NVLSVSFSPD-GRVVSSGSTDGTVRLWDLST 401
Query: 262 FKFKMTKQEHSRFVQAVRYSPSGSHFASAGFDGKVFLYDGASADLVSELGNPAHKGGVYA 321
H+ V ++ +SP G AS D + L+D K + +
Sbjct: 402 GSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWD--------------LKTSLKS 447
Query: 322 VAWKPDGTQLLTASGDKT 339
V++ PDG L + S D +
Sbjct: 448 VSFSPDGKVLASKSSDLS 465
Score = 46.2 bits (108), Expect = 4e-05
Identities = 30/133 (22%), Positives = 52/133 (39%), Gaps = 4/133 (3%)
Query: 552 NKSLSPKAELDHLGPVTDCSFSPSNEYLVASDAHRKVVLYRVPDFELAHNKEWGFHSAKV 611
+++ S + LGP + S + ++ + + H +
Sbjct: 9 SENKSKLLKKSELGPSLNSLSLLSLGSSESGILLLALLSDSLVSLPDLSSLLLRGHEDSI 68
Query: 612 NCVAWSPDSALVASGSLDTTIIIWSLASPAKHIIIKNAHPQSQITRLQWLDND----LLV 667
+A+SPD L+ SGS D TI +W L + K I S +++L D LL
Sbjct: 69 TSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDGNSILLA 128
Query: 668 SVGQDCNTKIWEI 680
S D K+W++
Sbjct: 129 SSSLDGTVKLWDL 141
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 48.1 bits (115), Expect = 1e-07
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 314 AHKGGVYAVAWKPDGTQLLTASGDKTCKLWD 344
H G V +VA+ PDG L + S D T ++WD
Sbjct: 9 GHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 47.0 bits (112), Expect = 2e-07
Identities = 15/30 (50%), Positives = 20/30 (66%)
Query: 607 HSAKVNCVAWSPDSALVASGSLDTTIIIWS 636
H+ V VA+SPD L+ASGS D T+ +W
Sbjct: 10 HTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 42.7 bits (101), Expect = 8e-06
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 393 TPIRVIKGHNKPITALALSPDRGTVFTGSHDGFITRWN 430
+R +KGH P+T++A SPD + +GS DG + W+
Sbjct: 2 KLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 39.6 bits (93), Expect = 1e-04
Identities = 14/39 (35%), Positives = 21/39 (53%)
Query: 262 FKFKMTKQEHSRFVQAVRYSPSGSHFASAGFDGKVFLYD 300
K T + H+ V +V +SP G+ AS DG V ++D
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 37.7 bits (88), Expect = 5e-04
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 80 IYTEHSCAVNVAKYSPSGFYIASGDISGKVRIWD 113
H+ V +SP G +ASG G VR+WD
Sbjct: 6 TLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 33.1 bits (76), Expect = 0.022
Identities = 11/39 (28%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 219 GTSVGEISGQSKPINSCDFKPSRPFRIITGSEDNTIAVF 257
G + + G + P+ S F P + +GS+D T+ V+
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNL-LASGSDDGTVRVW 38
Score = 30.4 bits (69), Expect = 0.17
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 563 HLGPVTDCSFSPSNEYLVASDAHRKVVLY 591
H GPVT +FSP L + V ++
Sbjct: 10 HTGPVTSVAFSPDGNLLASGSDDGTVRVW 38
Score = 25.8 bits (57), Expect = 9.5
Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 2/38 (5%)
Query: 642 KHIIIKNAHPQSQITRLQWL-DNDLLVSVGQDCNTKIW 678
K + H +T + + D +LL S D ++W
Sbjct: 2 KLLRTLKGH-TGPVTSVAFSPDGNLLASGSDDGTVRVW 38
>gnl|CDD|197651 smart00320, WD40, WD40 repeats. Note that these repeats are
permuted with respect to the structural repeats (blades)
of the beta propeller domain.
Length = 40
Score = 45.8 bits (109), Expect = 6e-07
Identities = 16/32 (50%), Positives = 19/32 (59%)
Query: 313 PAHKGGVYAVAWKPDGTQLLTASGDKTCKLWD 344
H G V +VA+ PDG L + S D T KLWD
Sbjct: 9 KGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 45.4 bits (108), Expect = 1e-06
Identities = 15/30 (50%), Positives = 19/30 (63%)
Query: 607 HSAKVNCVAWSPDSALVASGSLDTTIIIWS 636
H+ V VA+SPD +ASGS D TI +W
Sbjct: 11 HTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 44.2 bits (105), Expect = 3e-06
Identities = 15/40 (37%), Positives = 24/40 (60%)
Query: 391 PSTPIRVIKGHNKPITALALSPDRGTVFTGSHDGFITRWN 430
++ +KGH P+T++A SPD + +GS DG I W+
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 40.4 bits (95), Expect = 5e-05
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 261 PFKFKMTKQEHSRFVQAVRYSPSGSHFASAGFDGKVFLYD 300
+ T + H+ V +V +SP G + AS DG + L+D
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 39.2 bits (92), Expect = 1e-04
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 80 IYTEHSCAVNVAKYSPSGFYIASGDISGKVRIWD 113
H+ V +SP G Y+ASG G +++WD
Sbjct: 7 TLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 34.2 bits (79), Expect = 0.010
Identities = 11/41 (26%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 218 TGTSVGEISGQSKPINSCDFKPSRPFRIITGSEDNTIAVFE 258
+G + + G + P+ S F P + + +GS+D TI +++
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKY-LASGSDDGTIKLWD 40
Score = 30.0 bits (68), Expect = 0.29
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 563 HLGPVTDCSFSPSNEYLVASDAHRKVVLY 591
H GPVT +FSP +YL + + L+
Sbjct: 11 HTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
Score = 26.5 bits (59), Expect = 4.3
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 143 SIRNILVLSIGFYIASGDISGKVRIWD 169
+ ++ G Y+ASG G +++WD
Sbjct: 14 PVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 26.1 bits (58), Expect = 6.0
Identities = 7/31 (22%), Positives = 12/31 (38%), Gaps = 1/31 (3%)
Query: 650 HPQSQITRLQWL-DNDLLVSVGQDCNTKIWE 679
+T + + D L S D K+W+
Sbjct: 10 GHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 49.3 bits (117), Expect = 5e-06
Identities = 42/151 (27%), Positives = 71/151 (47%), Gaps = 13/151 (8%)
Query: 285 SHFASAGFDGKVFLYDGASADLVSELGNPAHKGGVYAVAW-KPDGTQLLTASGDKTCKLW 343
S AS+ F+G V ++D A + LV+E+ H+ V+++ + D T L + S D + KLW
Sbjct: 546 SQVASSNFEGVVQVWDVARSQLVTEMKE--HEKRVWSIDYSSADPTLLASGSDDGSVKLW 603
Query: 344 DIETKSVVSEFIMGNQVEDQQVSCLW----QGDYLLTVSLSGFISYLDVNNPSTPIRVIK 399
I VS +G + C+ G L S + Y D+ NP P+ +
Sbjct: 604 SINQG--VS---IGTIKTKANICCVQFPSESGRSLAFGSADHKVYYYDLRNPKLPLCTMI 658
Query: 400 GHNKPITALALSPDRGTVFTGSHDGFITRWN 430
GH+K ++ + D T+ + S D + W+
Sbjct: 659 GHSKTVSYVRFV-DSSTLVSSSTDNTLKLWD 688
Score = 35.4 bits (81), Expect = 0.096
Identities = 36/130 (27%), Positives = 60/130 (46%), Gaps = 14/130 (10%)
Query: 222 VGEISGQSKPINSCDFKPSRPFRIITGSEDNTI---AVFEGPPFKFKMTKQEHSRFVQAV 278
V E+ K + S D+ + P + +GS+D ++ ++ +G TK + V
Sbjct: 568 VTEMKEHEKRVWSIDYSSADPTLLASGSDDGSVKLWSINQGVSIGTIKTKAN----ICCV 623
Query: 279 RY-SPSGSHFASAGFDGKVFLYD--GASADLVSELGNPAHKGGVYAVAWKPDGTQLLTAS 335
++ S SG A D KV+ YD L + +G H V V + D + L+++S
Sbjct: 624 QFPSESGRSLAFGSADHKVYYYDLRNPKLPLCTMIG---HSKTVSYVRFV-DSSTLVSSS 679
Query: 336 GDKTCKLWDI 345
D T KLWD+
Sbjct: 680 TDNTLKLWDL 689
Score = 30.1 bits (67), Expect = 4.6
Identities = 18/74 (24%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 609 AKVNCVAWSPDSAL-VASGSLDTTIIIWSLASPAKHIIIKNAHPQSQITRLQWLDNDLLV 667
A + CV + +S +A GS D + + L +P + H ++ ++ ++++D+ LV
Sbjct: 618 ANICCVQFPSESGRSLAFGSADHKVYYYDLRNPKLPLCTMIGHSKT-VSYVRFVDSSTLV 676
Query: 668 SVGQDCNTKIWEIA 681
S D K+W+++
Sbjct: 677 SSSTDNTLKLWDLS 690
Score = 29.7 bits (66), Expect = 7.5
Identities = 29/122 (23%), Positives = 54/122 (44%), Gaps = 14/122 (11%)
Query: 526 SISLDHEHGLVAVGGADSKVHIYELN-----NKSLS-PKAELDHLGPVTDCSFSPSNEYL 579
+I D + A G + K+ I+E + + P EL ++ ++ +
Sbjct: 488 AIGFDRDGEFFATAGVNKKIKIFECESIIKDGRDIHYPVVELASRSKLSGICWNSYIKSQ 547
Query: 580 VASDAHRKVVLYRVPDFELAHNK---EWGFHSAKVNCVAWSP-DSALVASGSLDTTIIIW 635
VAS VV +++A ++ E H +V + +S D L+ASGS D ++ +W
Sbjct: 548 VASSNFEGVVQV----WDVARSQLVTEMKEHEKRVWSIDYSSADPTLLASGSDDGSVKLW 603
Query: 636 SL 637
S+
Sbjct: 604 SI 605
>gnl|CDD|173611 PTZ00421, PTZ00421, coronin; Provisional.
Length = 493
Score = 46.8 bits (111), Expect = 3e-05
Identities = 47/167 (28%), Positives = 73/167 (43%), Gaps = 20/167 (11%)
Query: 227 GQSKPINSCDFKPSRPFRIITGSEDNTIAVFEGPPFKFKMTK-------QEHSRFVQAVR 279
GQ PI F P P ++ T SED TI + P Q H++ V V
Sbjct: 73 GQEGPIIDVAFNPFDPQKLFTASEDGTIMGWGIPEEGLTQNISDPIVHLQGHTKKVGIVS 132
Query: 280 YSPSGSH-FASAGFDGKVFLYD---GASADLVSELGNPAHKGGVYAVAWKPDGTQLLTAS 335
+ PS + ASAG D V ++D G + +++ H + ++ W DG+ L T S
Sbjct: 133 FHPSAMNVLASAGADMVVNVWDVERGKAVEVIK-----CHSDQITSLEWNLDGSLLCTTS 187
Query: 336 GDKTCKLWDIETKSVVSEFIMGNQVEDQQVSCLW--QGDYLLTVSLS 380
DK + D ++VS + Q+ CLW + D ++T+ S
Sbjct: 188 KDKKLNIIDPRDGTIVSSVEAHASAKSQR--CLWAKRKDLIITLGCS 232
Score = 34.9 bits (80), Expect = 0.16
Identities = 50/270 (18%), Positives = 99/270 (36%), Gaps = 58/270 (21%)
Query: 316 KGGVYAVAWKP-DGTQLLTASGDKTCKLWDIETKSVVSEFIMGNQVEDQQVSCLWQGDYL 374
+G + VA+ P D +L TAS D T W I + +
Sbjct: 75 EGPIIDVAFNPFDPQKLFTASEDGTIMGWGIPEEGLTQ---------------------- 112
Query: 375 LTVSLSGFISYLDVNNPSTPIRVIKGHNKPITALALSPD-RGTVFTGSHDGFITRWNAKT 433
N S PI ++GH K + ++ P + + D + W+ +
Sbjct: 113 ---------------NISDPIVHLQGHTKKVGIVSFHPSAMNVLASAGADMVVNVWDVER 157
Query: 434 GENDRVQGAGHGNQINGMK--ATGELLYTCGIDDTIKQVDLSSN---AYSGPEVKLGSQP 488
G+ V H +QI ++ G LL T D + +D + SQ
Sbjct: 158 GKAVEVI-KCHSDQITSLEWNLDGSLLCTTSKDKKLNIIDPRDGTIVSSVEAHASAKSQR 216
Query: 489 RGLDIDENTLVTVTV-----KQISIVEN---GAKVSSLPIDYEPSSISL---DHEHGLVA 537
++ ++T+ +QI + + + S++ +D + S++ + D + L+
Sbjct: 217 CLWAKRKDLIITLGCSKSQQRQIMLWDTRKMASPYSTVDLD-QSSALFIPFFDEDTNLLY 275
Query: 538 VGG-ADSKVHIYELNNKSLSPKAELDHLGP 566
+G + + +EL N+ L+ + + P
Sbjct: 276 IGSKGEGNIRCFELMNERLTFCSSYSSVEP 305
>gnl|CDD|149648 pfam08662, eIF2A, Eukaryotic translation initiation factor eIF2A.
This is a family of eukaryotic translation initiation
factors.
Length = 194
Score = 37.6 bits (88), Expect = 0.008
Identities = 32/146 (21%), Positives = 48/146 (32%), Gaps = 28/146 (19%)
Query: 214 FMSETGTSVGEISGQSK-PINSCDFK---PSRPFRIITGSEDNTIAVFEG---PPFKFKM 266
+ ETG + + PI+ DF + F +I G I F+
Sbjct: 43 LIGETGGPDEVVELDKEGPIH--DFAWSPNGKEFAVIYGYMPAKITFFDLKGNVIHSLG- 99
Query: 267 TKQEHSRFVQAVRYSPSGSHFASAGF---DGKVFLYDGASADLVSELGNPAHKGGVYAVA 323
E R + +SP G AGF G++ +D ++
Sbjct: 100 ---EQPR--NTIFWSPFGRLVLLAGFGNLAGQIEFWD---VKNKKKIATAEASNATD-CE 150
Query: 324 WKPDGTQLLTASG------DKTCKLW 343
W PDG LTA+ D K+W
Sbjct: 151 WSPDGRYFLTATTSPRLRVDNGFKIW 176
Score = 36.5 bits (85), Expect = 0.019
Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 3/74 (4%)
Query: 54 PKGKNFLYTNGNSVIIRNIENPAISDIYTEHSCAVNVAKYSPSGFYIAS---GDISGKVR 110
P GK F G + + I++ N +SP G + G+++G++
Sbjct: 69 PNGKEFAVIYGYMPAKITFFDLKGNVIHSLGEQPRNTIFWSPFGRLVLLAGFGNLAGQIE 128
Query: 111 IWDTVNKEHILKNE 124
WD NK+ I E
Sbjct: 129 FWDVKNKKKIATAE 142
Score = 34.5 bits (80), Expect = 0.100
Identities = 31/111 (27%), Positives = 44/111 (39%), Gaps = 22/111 (19%)
Query: 91 AKYSPSG--FYIASGDISGKVRIWD-TVNKEHILKNEFHPIGGPIKDIGTLLSLTSIRNI 147
+SP+G F + G + K+ +D N H L P I S
Sbjct: 65 FAWSPNGKEFAVIYGYMPAKITFFDLKGNVIHSLGE------QPRNTI-----FWSPFGR 113
Query: 148 LVLSIGFYIASGDISGKVRIWDTVNKEHILKNEFHPIGGPIKDIAWSPDNQ 198
LVL GF G+++G++ WD NK+ I E D WSPD +
Sbjct: 114 LVLLAGF----GNLAGQIEFWDVKNKKKIATAE-ASNA---TDCEWSPDGR 156
Score = 29.2 bits (66), Expect = 5.1
Identities = 27/106 (25%), Positives = 40/106 (37%), Gaps = 14/106 (13%)
Query: 560 ELDHLGPVTDCSFSP-SNEYLV-ASDAHRKVVLYRVPDFELAHNKEWGFHSAKVNCVAWS 617
ELD GP+ D ++SP E+ V K+ + +L N N + WS
Sbjct: 55 ELDKEGPIHDFAWSPNGKEFAVIYGYMPAKITFF-----DLKGNVIHSLGEQPRNTIFWS 109
Query: 618 PDSALVAS---GSLDTTIIIWSLASPAKHIIIKNAHPQSQITRLQW 660
P LV G+L I W + + K I + T +W
Sbjct: 110 PFGRLVLLAGFGNLAGQIEFWDVKN--KKKIATAEASNA--TDCEW 151
>gnl|CDD|224423 COG1506, DAP2, Dipeptidyl aminopeptidases/acylaminoacyl-peptidases
[Amino acid transport and metabolism].
Length = 620
Score = 36.4 bits (84), Expect = 0.049
Identities = 53/328 (16%), Positives = 96/328 (29%), Gaps = 30/328 (9%)
Query: 273 RFVQAVRYSPSGSH--FASAGFDGKVFLYD-GASADLVSELGNPAHKGGVYAVAWKPDGT 329
V R SP G + G D LY + GGV + W PDG+
Sbjct: 13 ARVSDPRVSPPGGRLAYILTGLDFLKPLYKSSLWVSDGKTVRLLTFGGGVSELRWSPDGS 72
Query: 330 QLLTAS--GDKTCKLWDIETKSVVSEFIMGNQVEDQQVSCLWQGDYLLTVSLSGFISYLD 387
L S G + +L+ ++ ++++ V D + S GD + ++ G S D
Sbjct: 73 VLAFVSTDGGRVAQLYLVDVGGLITKTA--FGVSDARWS--PDGDRIAFLTAEG-ASKRD 127
Query: 388 VNNPSTPIRVI-----KGHNKPITALA--------LSPDRGTVFTGSHDGFITRWNAKTG 434
+ R+ +G + + L V + + DG R A
Sbjct: 128 GGDHLFVDRLPVWFDGRGGERSDLYVVDIESKLIKLGLGNLDVVSFATDGDG-RLVASIR 186
Query: 435 ENDRVQGAGHGNQINGMKATGELLYTCGIDDTIKQVDLSSNAYSGPEVKLGSQPRGLDID 494
D N ++ GEL + +I ++ + G + L +
Sbjct: 187 -LDDDADPWVTNLYVLIEGNGELESLTPGEGSISKLAFDA---DGKSIALLGTESDRGLA 242
Query: 495 ENTLVTVTVKQISIVENGAKVSSLPIDYEPSSISLDHEHGLVAVGGADSKVHIYELNNKS 554
E + + ++ V+ LD + L ++ +
Sbjct: 243 EGDFILLLDGELGEVDGDLSSGDDTRGAWAVEGGLDGDGLLFIATDGGGSSPLFRV--DD 300
Query: 555 LSPKAELDHLGPVTDCSFSPSNEYLVAS 582
L E F L +
Sbjct: 301 LGGGVEGLSGDDGGVPGFDVDGRKLALA 328
>gnl|CDD|227657 COG5354, COG5354, Uncharacterized protein, contains Trp-Asp (WD)
repeat [General function prediction only].
Length = 561
Score = 34.9 bits (80), Expect = 0.16
Identities = 40/206 (19%), Positives = 69/206 (33%), Gaps = 33/206 (16%)
Query: 251 DNTIAVFEGPPFKFKMTKQEHSRF-VQAVRYSPSGSHFASAGFDGKVFLYDGASADLVSE 309
I+VF + T+ E + V V SP G++ S G V + G S +
Sbjct: 10 SAVISVFWNSQSEVIHTRFESENWPVAYVSESPLGTYLFSEHAAG-VECWGGPSKAKLVR 68
Query: 310 LGNPAHKGGVYAVAWKPDGTQLLTAS---------------GDKTCKLWDIETKSVVSEF 354
+P V + + P+ L+T S +WDI + +V F
Sbjct: 69 FRHP----DVKYLDFSPNEKYLVTWSREPIIEPEIEISPFTSKNNVFVWDIASGMIVFSF 124
Query: 355 IMGNQVEDQQVSCLWQGD--YLLTVSLSGFISYLDVNNPS-TPIRVIKGHNKPITALALS 411
+Q + D Y+ V S + +N P + ++ I ++S
Sbjct: 125 NGISQPYLGWPVLKFSIDDKYVARVVGSSLYIHEITDNIEEHPFKNLRPVG--ILDFSIS 182
Query: 412 PDRGTVFTGSHDGFITRWNAKTGEND 437
P+ G+HD W +
Sbjct: 183 PE------GNHDELAY-WTPEKLNKP 201
>gnl|CDD|217409 pfam03178, CPSF_A, CPSF A subunit region. This family includes a
region that lies towards the C-terminus of the cleavage
and polyadenylation specificity factor (CPSF) A (160
kDa) subunit. CPSF is involved in mRNA polyadenylation
and binds the AAUAAA conserved sequence in pre-mRNA.
CPSF has also been found to be necessary for splicing of
single-intron pre-mRNAs. The function of the aligned
region is unknown but may be involved in RNA/DNA
binding.
Length = 318
Score = 34.5 bits (80), Expect = 0.17
Identities = 15/77 (19%), Positives = 25/77 (32%), Gaps = 4/77 (5%)
Query: 514 KVSSLPIDYEPSSISLDHEHGLVAVGGADSKVHIYELNNKSLSPKAELDHLGPVTDCSFS 573
V + +++ L G K+ +Y+L L PKA LD S
Sbjct: 79 LVHKTEVKGAVTALCEFQGRLLAGQG---QKLRVYDLGKDKLLPKAFLD-TPITYVVSLK 134
Query: 574 PSNEYLVASDAHRKVVL 590
++ D + V
Sbjct: 135 VFGNRIIVGDLMKSVTF 151
>gnl|CDD|189042 cd09872, PIN_Sll0205, PIN domain of the VapC-like Sll0205 protein
and homologs. Virulence associated protein C
(VapC)-like PIN (PilT N terminus) domain of the
Synechocystis sp. (strain PCC 6803) Sll0205 protein and
other uncharacterized homologs are included in this
subfamily. They are similar to the PIN domains of the
Mycobacterium tuberculosis VapC and Neisseria
gonorrhoeae FitB toxins of the prokaryotic
toxin/antitoxin operons, VapBC and FitAB, respectively,
which are believed to be involved in growth inhibition
by regulating translation. These toxins are nearly
always co-expressed with an antitoxin, a cognate protein
inhibitor, forming an inert protein complex.
Disassociation of the protein complex activates the
ribonuclease activity of the toxin by an, as yet
undefined mechanism. VapC-like PIN domains are homologs
of flap endonuclease-1 (FEN1)-like PIN domains, but lack
the extensive arch/clamp region and the H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region, seen in FEN1-like
PIN domains. PIN domains within this subgroup contain
four highly conserved acidic residues. These putative
active site residues are thought to bind Mg2+ and/or
Mn2+ ions and be essential for single-stranded
ribonuclease activity.
Length = 127
Score = 32.2 bits (74), Expect = 0.25
Identities = 13/54 (24%), Positives = 21/54 (38%), Gaps = 12/54 (22%)
Query: 628 LDTTIIIWSLASPAKHIIIKNAHPQSQITRLQWLDNDLLVSVGQDCNTKIWEIA 681
LDT ++W LA + ++ N++ VS +WEIA
Sbjct: 3 LDTHALLWWLADDPR-------LSPKARELIEDEANEVFVSA-----ISLWEIA 44
>gnl|CDD|187545 cd05234, UDP_G4E_2_SDR_e, UDP-glucose 4 epimerase, subgroup 2,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
archaeal and bacterial proteins, and has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 305
Score = 32.7 bits (75), Expect = 0.62
Identities = 23/64 (35%), Positives = 31/64 (48%), Gaps = 14/64 (21%)
Query: 480 PEVKLGSQPRGLDIDENTLVTVT---------VKQI-----SIVENGAKVSSLPIDYEPS 525
P+V+LG+ +D++EN L T VK+I S V AKV P DY P
Sbjct: 78 PDVRLGATDPDIDLEENVLATYNVLEAMRANGVKRIVFASSSTVYGEAKVIPTPEDYPPL 137
Query: 526 SISL 529
IS+
Sbjct: 138 PISV 141
>gnl|CDD|204739 pfam11768, DUF3312, Protein of unknown function (DUF3312). This is
a eukaryotic family of uncharacterized proteins. This
family shows similarity to WD40 repeat proteins.
Length = 544
Score = 30.5 bits (69), Expect = 3.1
Identities = 28/111 (25%), Positives = 44/111 (39%), Gaps = 22/111 (19%)
Query: 566 PVTDCSFSPSNEYLVASDAHRKVVLYRVPDFELAHNKEWGFHSAKV--NCVAWSPDSALV 623
V C+ SP E L+ +VLY H A V + +AW PDSA+V
Sbjct: 260 QVCSCARSPDEEKLLLGCIDSSLVLYD------EHRGVTLLAQAAVIPHLIAWHPDSAIV 313
Query: 624 ASGSLDTTIIIWSLA-SPAKH-IIIKNAHPQS------------QITRLQW 660
+ + + +A SP + ++ ++ P S + RLQW
Sbjct: 314 LVANEQGELQCFDIALSPIRMQLLSEDVTPSSTLDLSKYFVGSITLVRLQW 364
>gnl|CDD|222072 pfam13360, PQQ_2, PQQ-like domain. This domain contains several
repeats of the PQQ repeat.
Length = 234
Score = 30.1 bits (68), Expect = 3.2
Identities = 16/66 (24%), Positives = 22/66 (33%), Gaps = 7/66 (10%)
Query: 371 GDYLLTVSLSGFISYLDVNNPSTP-IRVIKGHNKPITALALSPDRGTVFTGSHDGFITRW 429
G + S G + LD+ R I N P D G +F DG +
Sbjct: 170 GGRVYASSYQGRLVALDLATGKVLWSREISSINGPA------VDGGLLFVVDDDGELVAL 223
Query: 430 NAKTGE 435
+ TG
Sbjct: 224 DRATGA 229
Score = 28.5 bits (64), Expect = 9.0
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 3/62 (4%)
Query: 413 DRGTVFTGSHDGFITRWNAKTGENDRVQGAGHGNQINGMKATGELLYTCGIDDTIKQVDL 472
D G V+ S+ G + + TG+ + ING G LL+ D + +D
Sbjct: 169 DGGRVYASSYQGRLVALDLATGKVLWSREIS---SINGPAVDGGLLFVVDDDGELVALDR 225
Query: 473 SS 474
++
Sbjct: 226 AT 227
>gnl|CDD|219547 pfam07741, BRF1, Brf1-like TBP-binding domain. This region covers
both the Brf homology II and III regions. This region is
involved in binding TATA binding protein.
Length = 95
Score = 28.4 bits (64), Expect = 3.2
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 108 KVRIWDTVNKEHILKNE 124
K RIWD +NK+++ + E
Sbjct: 17 KERIWDELNKDYLEEQE 33
Score = 28.4 bits (64), Expect = 3.2
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 164 KVRIWDTVNKEHILKNE 180
K RIWD +NK+++ + E
Sbjct: 17 KERIWDELNKDYLEEQE 33
>gnl|CDD|218251 pfam04762, IKI3, IKI3 family. Members of this family are
components of the elongator multi-subunit component of a
novel RNA polymerase II holoenzyme for transcriptional
elongation. This region contains WD40 like repeats.
Length = 903
Score = 30.3 bits (69), Expect = 3.8
Identities = 23/137 (16%), Positives = 49/137 (35%), Gaps = 15/137 (10%)
Query: 521 DYEPSSISLDHEHGLVAVGGAD-SKVHIYELNNKSLSP---KAELDHLGPVTDCSFSPSN 576
S +++G VAV D S + + L ++ P EL+ + D +FS SN
Sbjct: 366 TVARSPTLSPNDNGTVAV--IDGSTLLLTPLRLANVPPPMSARELELPSNINDVAFSKSN 423
Query: 577 EYLVASDAHRKVVLYRVPDFELAHNKEWGFHSAKVNCVAWSPDSALVASGSL-------- 628
+ + + +Y + ++K + + VA GSL
Sbjct: 424 SCVAVLTSDGDISIY-ELSLKKRKPGSPPKLTSKFSLDKVENSDSEVALGSLRQLAFLND 482
Query: 629 DTTIIIWSLASPAKHII 645
+++ + + ++
Sbjct: 483 SELLVLSDSDNITEIVL 499
Score = 30.0 bits (68), Expect = 5.9
Identities = 16/134 (11%), Positives = 35/134 (26%), Gaps = 25/134 (18%)
Query: 186 GPIKDIAWSPDNQRMVVVGEGRERFGHVFMSETGTS--------VGEISGQSKPINSCDF 237
I D+A+S N + V+ + ++ + S + +
Sbjct: 412 SNINDVAFSKSNSCVAVL--TSDGDISIYELSLKKRKPGSPPKLTSKFSLDKVENSDSEV 469
Query: 238 KPSRPFRIITGSEDNTIAVFEGPPFKFKMTKQEHSRFVQAVRYSPS------GSHFASAG 291
R + D+ + V ++ + + S +S
Sbjct: 470 ALGSL-RQLAFLNDSELLVLSDSDNITEIVLVDVDDTENPLSVSVITEIEGIVLILSSND 528
Query: 292 F--------DGKVF 297
+ DGKV
Sbjct: 529 YKHVYIETRDGKVL 542
>gnl|CDD|220133 pfam09177, Syntaxin-6_N, Syntaxin 6, N-terminal. Members of this
family, which are found in the amino terminus of various
SNARE proteins, adopt a structure consisting of an
antiparallel three-helix bundle. Their exact function
has not been determined, though it is known that they
regulate the SNARE motif, as well as mediate various
protein-protein interactions involved in
membrane-transport.
Length = 96
Score = 28.4 bits (64), Expect = 4.1
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 251 DNTIAVFEGPPFKFKMTKQE---HSRFVQAVR 279
+ ++V E P KF + ++E RFV +R
Sbjct: 58 EEAVSVVEANPEKFGLDEEEISRRRRFVAEIR 89
>gnl|CDD|240485 cd12905, SPRY_PRY_TRIM_Bty_69_NF7, PRY/SPRY domain in tripartite
motif-containing protein 69 (TRIM69), Bloodthirsty (bty)
and NF7. This domain, consisting of the distinct
N-terminal PRY subdomain followed by the SPRY subdomain,
is found at the C-terminus of TRIM69 and TRIM proteins
NF7 and bloodthirsty (bty). TRIM69 is a novel testis E3
ubiquitin ligase that may function to ubiquitinate its
particular substrates during spermatogenesis. In humans,
TRIM69 localizes in the cytoplasm and nucleus, and
requires an intact RING finger domain to function. TRIM
protein NF7, which also contains a chromodomain (CHD) at
the N-terminus and an RFP (Ret finger protein)-like
domain at the C-terminus, is required for its
association with transcriptional units of RNA polymerase
II which is mediated by a trimeric B box. In Xenopus
oocyte, xNF7 has been identified as a nuclear
microtubule-associated protein (MAP) whose
microtubule-bundling activity, but not E3-ligase
activity, contributes to microtubule organization and
spindle integrity. Bloodthirsty (bty) is a novel gene
identified in zebrafish and has been shown to likely
play a role in in regulation of the terminal steps of
erythropoiesis.
Length = 176
Score = 29.2 bits (66), Expect = 4.7
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 526 SISLDHEHGLVAVGGADSKVHIY 548
+ LD+E G V+ AD+ HIY
Sbjct: 123 GVFLDYEGGQVSFYDADTMTHIY 145
>gnl|CDD|225926 COG3391, COG3391, Uncharacterized conserved protein [Function
unknown].
Length = 381
Score = 29.5 bits (66), Expect = 6.4
Identities = 32/161 (19%), Positives = 48/161 (29%), Gaps = 16/161 (9%)
Query: 180 EFHPIGGPIKDIAWSPDNQRMVVVGEG-RERFGHVFMSETGTSVGEISGQSKPINSCDFK 238
P+G +A PD + + V G V + T I + P
Sbjct: 110 GSIPVGLGPVGLAVDPDGKYVYVANAGNGNNTVSVIDAATNKVTATIPVGNTPTGV-AVD 168
Query: 239 PSRPFRIITGSEDNTIAVFEGPPFKFKMTKQEHSRFVQAVRYSPSGSHFASAG------- 291
P +T S+DNT++V + + + V P+G G
Sbjct: 169 PDGNKVYVTNSDDNTVSVID---TSGNSVVRGSVGSLVGVGTGPAGIAVDPDGNRVYVAN 225
Query: 292 ---FDGKVFLYDGASADLVSELGNPAHKGGVYAVAWKPDGT 329
V D A+ V+ P G VA P G
Sbjct: 226 DGSGSNNVLKIDTAT-GNVTATDLPVGSGAPRGVAVDPAGK 265
>gnl|CDD|240492 cd13734, SPRY_PRY_C-I, PRY/SPRY domain in tripartite
motif-containing proteins 1, 9, 18, 36, 46, 67,76
(TRIM1, TRIM9, TRIM18, TRIM36, TRIM46, TRIM67, TRIM76).
This domain, consisting of the distinct N-terminal PRY
subdomain followed by the SPRY subdomain, is found at
the C-terminus of several Class I TRIM proteins,
including TRIM1, TRIM9, TRIM18, TRIM36, TRIM46, TRIM67
and TRIM76. TRIM1 (also known as MID2) and its close
homolog, TRIM18 (also known as MID1), both contain a
B30.2-like domain at their C-terminus and a single
fibronectin type III (FN3) motif between it and their
N-terminal RBCC domain. Their coiled-coil motifs mediate
both homo- and heterodimerization, a prerequisite for
association of the rapamycin-sensitive PP2A regulatory
subunit Alpha 4 with microtubules. Mutations in TRIM18
have shown to cause Opitz syndrome, a disorder causing
congenital anomalies such as cleft lip and palate as
well as heart defects. TRIM9 is expressed mainly in the
cerebral cortex, and functions as an E3 ubiquitin
ligase. Its immunoreactivity is severely decreased in
affected brain areas in Parkinson's disease and dementia
with Lewy bodies, possibly playing an important role in
the regulation of neuronal function and participating in
pathological process of Lewy body disease through its
ligase. TRIM36 interacts with centromere protein-H, one
of the kinetochore proteins and possibly associates with
chromosome segregation; an excess of TRIM36 may cause
chromosomal instability. TRIM46 has not yet been
characterized. TRIM67 negatively regulates Ras activity
via degradation of 80K-H, leading to neural
differentiation, including neuritogenesis. TRIM76 (also
known as cardiomyopathy-associated protein 5 or CMYA5)
is a muscle-specific member of the TRIM superfamily, but
lacks the RING domain. It is possibly involved in
protein kinase A signaling as well as vesicular
trafficking. It has also been implicated in Duchenne
muscular dystrophy and cardiac disease.
Length = 169
Score = 28.8 bits (65), Expect = 7.1
Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 514 KVSSLPIDYEPSSIS--LDHEHGLVAVGGADSKVHIYELNNK 553
KV L + P I LD++ G ++ A+SK H++ +
Sbjct: 107 KVVDLTVTPHPRRIGVLLDYDRGTLSFYDAESKQHLHTFHVD 148
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 29.5 bits (66), Expect = 7.5
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 307 VSELGNP-----AHKGGVYAVAWKPDGTQLLTASG-DKTCKLWDIETKSVVSEFIM 356
V E+ +P HK + + W P ++ +SG D +WDIE + + M
Sbjct: 111 VKEIKDPQCILKGHKKKISIIDWNPMNYYIMCSSGFDSFVNIWDIENEKRAFQINM 166
>gnl|CDD|132862 cd07223, Pat_PNPLA5-mammals, Patatin-like phospholipase domain
containing protein 5. PNPLA5, also known as GS2L
(GS2-like), plays a role in regulation of adipocyte
differentiation. PNPLA5 is expressed in brain tissue in
high mRNA levels and low levels in liver tissue. There
is no concrete evidence in support of the enzymatic
activity of GS2L. This family includes patatin-like
proteins: GS2L (GS2-like) and PNPLA5 (Patatin-like
phospholipase domain-containing protein 5) reported
exclusively in mammals.
Length = 405
Score = 29.1 bits (65), Expect = 8.7
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 6/79 (7%)
Query: 511 NGAKVSSLPIDYEPSSISLDHEHGLVAVGGADSKVHIYELN--NKSLSPKAELDHLGPVT 568
+GA ++LP PS+I++ HG V + + +++ELN N S LG
Sbjct: 168 DGALSNNLPFSDCPSTITVSPFHGTVDICPQSTSANLHELNAFNASFQISTRNFFLG--L 225
Query: 569 DCSFSPSNEYLVASDAHRK 587
C P E V +D R+
Sbjct: 226 KCLIPPKPE--VVADNCRQ 242
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.135 0.410
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 34,698,384
Number of extensions: 3400985
Number of successful extensions: 2749
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2610
Number of HSP's successfully gapped: 76
Length of query: 683
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 580
Effective length of database: 6,369,140
Effective search space: 3694101200
Effective search space used: 3694101200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 62 (27.7 bits)