RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4876
(609 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 = 141 bits (357), Expect = 9e-38
Identities = 74/248 (29%), Positives = 120/248 (48%), Gaps = 15/248 (6%)
Query: 338 VCSVAWIQEGYMLGVGTSLGTVQLWDVSAKKKCRTMDGHDVRVGALAW--NTYILSSGSR 395
V VA +G L G+S T++LWD+ + RT+ GH V ++A+ + ILSS SR
Sbjct: 54 VRDVAASADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSR 113
Query: 396 CGNIVHHDVRSRDHKVALLQNHTQEVCGLKWSPDGRYLASGGNDNLLNIWSGVPGQHTFS 455
I DV + + L+ HT V + +SPDG ++AS D + +W G+
Sbjct: 114 DKTIKVWDVETGK-CLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGK---- 168
Query: 456 TQPIHSLSRHQAAVKAIAWCPWSPNVLASGGGTADRHIYFWNVSSGACLDSIDTKSQ-VC 514
+ +L+ H V ++A+ P +L+S D I W++S+G CL ++ V
Sbjct: 169 --CVATLTGHTGEVNSVAFSPDGEKLLSSSS---DGTIKLWDLSTGKCLGTLRGHENGVN 223
Query: 515 ALLWNSDYKELVSAHGFAQNQLIIWKYPSLVKVAELHGHSARVLNLAMSPDETTVLSAGA 574
++ ++ D L S + +W + V L GH+ V +LA SPD + S A
Sbjct: 224 SVAFSPDGYLLASGS--EDGTIRVWDLRTGECVQTLSGHTNSVTSLAWSPDGKRLASGSA 281
Query: 575 DETLRLWK 582
D T+R+W
Sbjct: 282 DGTIRIWD 289
Score = 120 bits (303), Expect = 2e-30
Identities = 66/249 (26%), Positives = 118/249 (47%), Gaps = 19/249 (7%)
Query: 338 VCSVAWIQEGYMLGVGTSLGTVQLWDVSAKKKCRTMDGH---DVRVGALAWNTYILSSGS 394
V VA+ +G +L G+ GT+++WD+ + RT+ GH V A A TY+ S S
Sbjct: 12 VTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSS 71
Query: 395 -RCGNIVHHDVRSRDHKVALLQNHTQEVCGLKWSPDGRYLASGGNDNLLNIWSGVPGQHT 453
+ + D+ + V L HT V + +SPDGR L+S D + +W
Sbjct: 72 DKTIRL--WDLET-GECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVW------DV 122
Query: 454 FSTQPIHSLSRHQAAVKAIAWCPWSPNVLASGGGTADRHIYFWNVSSGACLDSIDT-KSQ 512
+ + + +L H V ++A+ P +AS D I W++ +G C+ ++ +
Sbjct: 123 ETGKCLTTLRGHTDWVNSVAFSP-DGTFVASSS--QDGTIKLWDLRTGKCVATLTGHTGE 179
Query: 513 VCALLWNSDYKELVSAHGFAQNQLIIWKYPSLVKVAELHGHSARVLNLAMSPDETTVLSA 572
V ++ ++ D ++L+S + + +W + + L GH V ++A SPD + S
Sbjct: 180 VNSVAFSPDGEKLLS--SSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASG 237
Query: 573 GADETLRLW 581
D T+R+W
Sbjct: 238 SEDGTIRVW 246
Score = 90.9 bits (226), Expect = 4e-20
Identities = 57/177 (32%), Positives = 83/177 (46%), Gaps = 33/177 (18%)
Query: 275 IDWSHFN--VLAVALGGSIYLWNGESDSNSKYIICQSPLVQELTSKCIQDNRAIDHLMDL 332
+ +S V + + G+I LW+ T KC+ L
Sbjct: 141 VAFSPDGTFVASSSQDGTIKLWDLR------------------TGKCVAT---------L 173
Query: 333 EG-NENVCSVAWIQEGYMLGVGTSLGTVQLWDVSAKKKCRTMDGHDVRVGALAW--NTYI 389
G V SVA+ +G L +S GT++LWD+S K T+ GH+ V ++A+ + Y+
Sbjct: 174 TGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYL 233
Query: 390 LSSGSRCGNIVHHDVRSRDHKVALLQNHTQEVCGLKWSPDGRYLASGGNDNLLNIWS 446
L+SGS G I D+R+ + V L HT V L WSPDG+ LASG D + IW
Sbjct: 234 LASGSEDGTIRVWDLRTGE-CVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 78.1 bits (193), Expect = 7e-16
Identities = 39/170 (22%), Positives = 67/170 (39%), Gaps = 52/170 (30%)
Query: 414 LQNHTQEVCGLKWSPDGRYLASGGNDNLLNIWSGVPGQHTFSTQPIHSLSRHQAAVKAIA 473
L+ HT V + +SPDG+ LA+G D + +W + + + +L H V+ +A
Sbjct: 5 LKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWD------LETGELLRTLKGHTGPVRDVA 58
Query: 474 WCPWSPNVLASGGGTADRHIYFWNVSSGACLDSIDTKSQVCALLWNSDYKELVSAHGFAQ 533
LASG D+ I W++ +G C
Sbjct: 59 ASADG-TYLASGSS--DKTIRLWDLETGEC------------------------------ 85
Query: 534 NQLIIWKYPSLVKVAELHGHSARVLNLAMSPDETTVLSAGADETLRLWKI 583
V L GH++ V ++A SPD + S+ D+T+++W +
Sbjct: 86 -------------VRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDV 122
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 121 bits (303), Expect = 2e-29
Identities = 76/262 (29%), Positives = 132/262 (50%), Gaps = 11/262 (4%)
Query: 338 VCSVAWIQEGYMLGVGTSL-GTVQLWDVSAKKKCR-TMDGH-DVRVGALAWNTYILSSGS 394
V S+A+ +G +L S GT++LWD+S K R T+ GH D V + + + +L+SGS
Sbjct: 201 VSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSSFSPDGSLLASGS 260
Query: 395 RCGNIVHHDVRSRDHKVALLQNHTQEVCGLKWSPDGRYLASGGNDNLLNIWSGVPGQHTF 454
G I D+RS + L H+ V + +SPDG+ LASG +D + +W G
Sbjct: 261 SDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETG---- 316
Query: 455 STQPIHSLSRHQAAVKAIAWCPWSPNVLASGGGTADRHIYFWNVSSGACLDSIDTKSQVC 514
+L H+ V ++++ P +++ GG+ D I W++ +G L +++ S V
Sbjct: 317 KLLSSLTLKGHEGPVSSLSFSPDGSLLVS--GGSDDGTIRLWDLRTGKPLKTLEGHSNVL 374
Query: 515 ALLWNSDYKELVSAHGFAQNQLIIWKYPSLVKVAELHGHSARVLNLAMSPDETTVLSAGA 574
++ ++ D V + G + +W + + L GH++RV +L SPD ++ S +
Sbjct: 375 SVSFSPD--GRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSS 432
Query: 575 DETLRLWKIFEKVKSKKKEIKN 596
D T+RLW + +KS
Sbjct: 433 DNTIRLWDLKTSLKSVSFSPDG 454
Score = 94.8 bits (234), Expect = 1e-20
Identities = 82/309 (26%), Positives = 150/309 (48%), Gaps = 20/309 (6%)
Query: 306 ICQSPLVQELTSKCIQDNRAIDHLMDLEGNENVCSVAWIQEGYMLGVGTSLGTVQLWDVS 365
L+ L S + + L+ +++ S+A+ +G +L G+S GT++LWD+
Sbjct: 36 SESGILLLALLSDSLVSLPDLSSLLLRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLD 95
Query: 366 AKKKC-RTMDG-HDVRVGALAW-----NTYILSSGSRCGNIVHHDVRSRDHKVALLQNHT 418
+K ++++G HD V LA N+ +L+S S G + D+ + + L+ H+
Sbjct: 96 NGEKLIKSLEGLHDSSVSKLALSSPDGNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHS 155
Query: 419 QEVCGLKWSPDGRYLASGGN-DNLLNIWSGVPGQHTFSTQPIHSLSRHQAAVKAIAWCPW 477
+ V L +SPDG+ LASG + D + +W + +P+ +L+ H V ++A+ P
Sbjct: 156 ESVTSLAFSPDGKLLASGSSLDGTIKLWD------LRTGKPLSTLAGHTDPVSSLAFSPD 209
Query: 478 SPNVLASGGGTADRHIYFWNVSSGACL-DSIDTKSQVCALLWNSDYKELVSAHGFAQNQL 536
++ASG +D I W++S+G L ++ S ++ D L S G + +
Sbjct: 210 GGLLIASGS--SDGTIRLWDLSTGKLLRSTLSGHSDSVVSSFSPDGSLLAS--GSSDGTI 265
Query: 537 IIWKYPSLVK-VAELHGHSARVLNLAMSPDETTVLSAGADETLRLWKIFEKVKSKKKEIK 595
+W S + L GHS+ VL++A SPD + S +D T+RLW + +K
Sbjct: 266 RLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLK 325
Query: 596 NNASKFNSM 604
+ +S+
Sbjct: 326 GHEGPVSSL 334
Score = 71.3 bits (173), Expect = 4e-13
Identities = 53/248 (21%), Positives = 102/248 (41%), Gaps = 15/248 (6%)
Query: 367 KKKCRTMDGHDVRVGALAWNT---YILSSGSRCGNIVHHDVRSRDHKVALLQNHTQEVCG 423
+ GH+ + ++A++ +LS S + +L H V
Sbjct: 55 DLSSLLLRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSK 114
Query: 424 LKW-SPDGRYLAS--GGNDNLLNIWSGVPGQHTFSTQPIHSLSRHQAAVKAIAWCPWSPN 480
L SPDG + D + +W + + I +L H +V ++A+ P
Sbjct: 115 LALSSPDGNSILLASSSLDGTVKLW-----DLSTPGKLIRTLEGHSESVTSLAFSP-DGK 168
Query: 481 VLASGGGTADRHIYFWNVSSGACLDSIDTKSQVCALLWNSDYKELVSAHGFAQNQLIIWK 540
+LASG D I W++ +G L ++ + + L S L+ A G + + +W
Sbjct: 169 LLASGSS-LDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWD 227
Query: 541 YPS-LVKVAELHGHSARVLNLAMSPDETTVLSAGADETLRLWKIFEKVKSKKKEIKNNAS 599
+ + + L GHS V++ + SPD + + S +D T+RLW + + +++S
Sbjct: 228 LSTGKLLRSTLSGHSDSVVS-SFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSS 286
Query: 600 KFNSMFNS 607
+ F+
Sbjct: 287 VLSVAFSP 294
Score = 69.7 bits (169), Expect = 1e-12
Identities = 48/212 (22%), Positives = 83/212 (39%), Gaps = 8/212 (3%)
Query: 375 GHDVRVGALAWNTYILSSGSRCGNIVHHDVRSRDHKVALLQNHTQEVCGLKWSPDGRYLA 434
G + +L S + V D LL+ H + + +SPDG L
Sbjct: 22 GPSLNSLSLLSLGSSESGILLLALLSDSLVSLPDLSSLLLRGHEDSITSIAFSPDGELLL 81
Query: 435 SGGNDNLLNIWSGVPGQHTFSTQPIHSLSRHQAAVKAIAWCPWSPNVLASGGGTADRHIY 494
SG +D + +W G+ + H ++V +A N + + D +
Sbjct: 82 SGSSDGTIKLWDLDNGEKLIKSL----EGLHDSSVSKLALSSPDGNSILLASSSLDGTVK 137
Query: 495 FWNVSSGACLDSI--DTKSQVCALLWNSDYKELVSAHGFAQNQLIIWKYPSLVKVAELHG 552
W++S+ L V +L ++ D K L S + +W + ++ L G
Sbjct: 138 LWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLD-GTIKLWDLRTGKPLSTLAG 196
Query: 553 HSARVLNLAMSPD-ETTVLSAGADETLRLWKI 583
H+ V +LA SPD + S +D T+RLW +
Sbjct: 197 HTDPVSSLAFSPDGGLLIASGSSDGTIRLWDL 228
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 47.0 bits (112), Expect = 2e-07
Identities = 14/37 (37%), Positives = 21/37 (56%)
Query: 410 KVALLQNHTQEVCGLKWSPDGRYLASGGNDNLLNIWS 446
+ L+ HT V + +SPDG LASG +D + +W
Sbjct: 3 LLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 41.6 bits (98), Expect = 2e-05
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 545 VKVAELHGHSARVLNLAMSPDETTVLSAGADETLRLWK 582
+ L GH+ V ++A SPD + S D T+R+W
Sbjct: 2 KLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 36.9 bits (86), Expect = 9e-04
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 457 QPIHSLSRHQAAVKAIAWCPWSPNVLASGGGTADRHIYFWN 497
+ + +L H V ++A+ P N+LASG D + W+
Sbjct: 2 KLLRTLKGHTGPVTSVAFSPDG-NLLASGS--DDGTVRVWD 39
Score = 28.1 bits (63), Expect = 1.1
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 335 NENVCSVAWIQEGYMLGVGTSLGTVQLWD 363
V SVA+ +G +L G+ GTV++WD
Sbjct: 11 TGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
>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 = 46.2 bits (110), Expect = 5e-07
Identities = 15/38 (39%), Positives = 23/38 (60%)
Query: 409 HKVALLQNHTQEVCGLKWSPDGRYLASGGNDNLLNIWS 446
+ L+ HT V + +SPDG+YLASG +D + +W
Sbjct: 3 ELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 41.5 bits (98), Expect = 2e-05
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 543 SLVKVAELHGHSARVLNLAMSPDETTVLSAGADETLRLWK 582
S + L GH+ V ++A SPD + S D T++LW
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 38.4 bits (90), Expect = 2e-04
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 3/43 (6%)
Query: 455 STQPIHSLSRHQAAVKAIAWCPWSPNVLASGGGTADRHIYFWN 497
S + + +L H V ++A+ P LASG D I W+
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDG-KYLASGS--DDGTIKLWD 40
Score = 26.5 bits (59), Expect = 4.1
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 335 NENVCSVAWIQEGYMLGVGTSLGTVQLWD 363
V SVA+ +G L G+ GT++LWD
Sbjct: 12 TGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 46.2 bits (109), Expect = 4e-05
Identities = 36/153 (23%), Positives = 77/153 (50%), Gaps = 13/153 (8%)
Query: 433 LASGGNDNLLNIWSGVPGQHTFSTQPIHSLSRHQAAVKAIAWCPWSPNVLASGGGTADRH 492
+AS + ++ +W +Q + + H+ V +I + P +LASG + D
Sbjct: 548 VASSNFEGVVQVWD------VARSQLVTEMKEHEKRVWSIDYSSADPTLLASG--SDDGS 599
Query: 493 IYFWNVSSGACLDSIDTKSQVCALLWNSDYKELVSAHGFAQNQLIIW--KYPSLVKVAEL 550
+ W+++ G + +I TK+ +C + + S+ + A G A +++ + + P L + +
Sbjct: 600 VKLWSINQGVSIGTIKTKANICCVQFPSESGRSL-AFGSADHKVYYYDLRNPKL-PLCTM 657
Query: 551 HGHSARVLNLAMSPDETTVLSAGADETLRLWKI 583
GHS + ++ D +T++S+ D TL+LW +
Sbjct: 658 IGHS-KTVSYVRFVDSSTLVSSSTDNTLKLWDL 689
Score = 38.1 bits (88), Expect = 0.015
Identities = 24/90 (26%), Positives = 48/90 (53%), Gaps = 2/90 (2%)
Query: 509 TKSQVCALLWNSDYKELVSAHGFAQNQLIIWKYPSLVKVAELHGHSARVLNLAMSPDETT 568
++S++ + WNS K V++ F + + +W V E+ H RV ++ S + T
Sbjct: 531 SRSKLSGICWNSYIKSQVASSNF-EGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSADPT 589
Query: 569 VLSAGADE-TLRLWKIFEKVKSKKKEIKNN 597
+L++G+D+ +++LW I + V + K N
Sbjct: 590 LLASGSDDGSVKLWSINQGVSIGTIKTKAN 619
Score = 37.8 bits (87), Expect = 0.017
Identities = 56/271 (20%), Positives = 100/271 (36%), Gaps = 65/271 (23%)
Query: 320 IQDNRAIDH-LMDLEGNENVCSVAWIQEGYM---LGVGTSLGTVQLWDVSAKKKCRTMDG 375
I+D R I + +++L + + W Y+ + G VQ+WDV+ + M
Sbjct: 516 IKDGRDIHYPVVELASRSKLSGICW--NSYIKSQVASSNFEGVVQVWDVARSQLVTEMKE 573
Query: 376 HDVRVGALAWNT---YILSSGSRCGNIVHHDVR--------------------------- 405
H+ RV ++ +++ +L+SGS G++ +
Sbjct: 574 HEKRVWSIDYSSADPTLLASGSDDGSVKLWSINQGVSIGTIKTKANICCVQFPSESGRSL 633
Query: 406 ---SRDHKVAL--LQN----------HTQEVCGLKWSPDGRYLASGGNDNLLNIWSGVPG 450
S DHKV L+N H++ V +++ D L S DN L +W
Sbjct: 634 AFGSADHKVYYYDLRNPKLPLCTMIGHSKTVSYVRFV-DSSTLVSSSTDNTLKLWDLSMS 692
Query: 451 QHTFSTQPIHSLSRHQAAVKAIAWCPWSPNVLASGGGTADRHIY------------FWNV 498
+ P+HS H VK S +A+G T + +Y F +
Sbjct: 693 ISGINETPLHSFMGH-TNVKNFVGLSVSDGYIATGSETNEVFVYHKAFPMPVLSYKFKTI 751
Query: 499 SSGACLDSIDTKSQVCALLWNSDYKELVSAH 529
+ L+ D + ++ W LV+A+
Sbjct: 752 DPVSGLEVDDASQFISSVCWRGQSSTLVAAN 782
>gnl|CDD|173611 PTZ00421, PTZ00421, coronin; Provisional.
Length = 493
Score = 35.3 bits (81), Expect = 0.10
Identities = 24/65 (36%), Positives = 34/65 (52%), Gaps = 3/65 (4%)
Query: 458 PIHSLSRHQAAVKAIAWCPWSPNVLASGGGTADRHIYFWNVSSGACLDSIDTKS-QVCAL 516
PI L H V +++ P + NVLAS G AD + W+V G ++ I S Q+ +L
Sbjct: 117 PIVHLQGHTKKVGIVSFHPSAMNVLASAG--ADMVVNVWDVERGKAVEVIKCHSDQITSL 174
Query: 517 LWNSD 521
WN D
Sbjct: 175 EWNLD 179
Score = 31.0 bits (70), Expect = 1.8
Identities = 37/152 (24%), Positives = 60/152 (39%), Gaps = 18/152 (11%)
Query: 368 KKCRTMDGHDVRVGALAWNTYILSSGS-RCGNIVHHDVRSRDHKVALLQNHTQEVCGLKW 426
KK + H + LA S+G+ N+ DV R V +++ H+ ++ L+W
Sbjct: 126 KKVGIVSFHPSAMNVLA------SAGADMVVNV--WDVE-RGKAVEVIKCHSDQITSLEW 176
Query: 427 SPDGRYLASGGNDNLLNIWSGVPGQHTF-STQPIHSLSRHQAAVKAIAWCPWSPNVLASG 485
+ DG L + D LNI P T S+ H+ ++ Q + W ++ G
Sbjct: 177 NLDGSLLCTTSKDKKLNIID--PRDGTIVSSVEAHASAKSQRCL----WAKRKDLIITLG 230
Query: 486 GGTAD-RHIYFWNVSSGACLDSIDTKSQVCAL 516
+ R I W+ A S Q AL
Sbjct: 231 CSKSQQRQIMLWDTRKMASPYSTVDLDQSSAL 262
>gnl|CDD|233496 TIGR01622, SF-CC1, 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.
Length = 457
Score = 34.1 bits (78), Expect = 0.19
Identities = 19/94 (20%), Positives = 33/94 (35%), Gaps = 23/94 (24%)
Query: 65 RKRSQSVGRKTPKTPKKSPGRHKSNPNTPS-------------------AKSKTPSGGDR 105
R R + GR T + GR +S + S ++S++P+ R
Sbjct: 1 RYRDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYR 60
Query: 106 YIPNRSAIDTELSHYLLTRDENMEDLSPSEREKR 139
+RS + E L+ +ER+ R
Sbjct: 61 PRGDRSYRRDDRRS----GRNTKEPLTEAERDDR 90
>gnl|CDD|132374 TIGR03331, SAM_DCase_Eco, S-adenosylmethionine decarboxylase
proenzyme, Escherichia coli form. Members of this
protein family are the single chain precursor of the
S-adenosylmethionine decarboxylase as found in
Escherichia coli. This form shows a substantially
different architecture from the form shared by the
Archaea, Bacillus, and many other species (TIGR03330).
It shows little or no similarity to the form found in
eukaryotes (TIGR00535) [Central intermediary metabolism,
Polyamine biosynthesis].
Length = 259
Score = 32.7 bits (75), Expect = 0.39
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 7/43 (16%)
Query: 114 DTELSHYLLTRDENMEDLSPSEREK-----RKAMSELVHGKDI 151
D +L +YL EDLSP ER + +K M E+ +G++I
Sbjct: 219 DFDLDNYLF--GTAKEDLSPEERREITARLKKEMLEIFYGRNI 259
>gnl|CDD|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases [Signal transduction
mechanisms].
Length = 1175
Score = 32.2 bits (73), Expect = 1.2
Identities = 31/128 (24%), Positives = 49/128 (38%), Gaps = 12/128 (9%)
Query: 17 DEPLTKGPLPRWQRKNKENSSVEMNMSNFNSSNSMSSSDLNKSRGNEERKRSQSVGRKTP 76
D ++K LP + + K N N ++ + NS S K +
Sbjct: 24 DAFVSKQLLPPRRLQRKLNPISIRNGADNDIINSESKESFGKY------ALGHQIFSSFS 77
Query: 77 KTPKKSPGRHKSNPNT--PSAKSKTPSG----GDRYIPNRSAIDTELSHYLLTRDENMED 130
+PK R+ + P T PSA S T S GD++ P ++ S +D D
Sbjct: 78 SSPKLFQRRNSAGPITHSPSATSSTSSLNSNDGDQFSPASDSLSFNPSSTQSRKDSGPGD 137
Query: 131 LSPSEREK 138
SP ++ K
Sbjct: 138 GSPVQKRK 145
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 31.1 bits (70), Expect = 1.8
Identities = 19/51 (37%), Positives = 35/51 (68%), Gaps = 2/51 (3%)
Query: 547 VAELHGHSARVLNLAMSPDETTVLSAGA-DETLRLWKIFEKVKSKKKEIKN 596
V +L GH++ +L+L +P + +L++G+ D T+R+W+I +S KEIK+
Sbjct: 67 VIKLKGHTSSILDLQFNPCFSEILASGSEDLTIRVWEIPHNDES-VKEIKD 116
>gnl|CDD|199837 cd10279, PQQ_ADH_II, PQQ_like domain of the quinohemoprotein
alcohol dehydrogenase (type II). This family of
monomeric and soluble type II alcohol dehydrogenases
utilizes pyrroloquinoline quinone (PQQ) as a cofactor
and is related to ethanol, methanol, and membrane-bound
glucose dehydrogenases. The alignment model contains an
8-bladed beta-propeller.
Length = 549
Score = 31.1 bits (71), Expect = 1.9
Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 5/45 (11%)
Query: 476 PWSPNVLASGG-----GTADRHIYFWNVSSGACLDSIDTKSQVCA 515
PW+ VLA+ G GTAD + ++ +G L S DT S + A
Sbjct: 451 PWNGGVLATAGNLVFQGTADGELAAYDARTGEKLWSFDTGSGIVA 495
>gnl|CDD|234229 TIGR03490, Mycoplas_LppA, mycoides cluster lipoprotein, LppA/P72
family. Members of this protein family occur in
Mycoplasma mycoides, Mycoplasma hyopneumoniae, and
related Mycoplasmas in small paralogous families that
may also include truncated forms and/or pseudogenes.
Members are predicted lipoproteins with a conserved
signal peptidase II processing and lipid attachment
site. Note that the name for certain characterized
members, p72, reflects an anomalous apparent molecular
weight, given a theoretical MW of about 61 kDa.
Length = 541
Score = 30.6 bits (69), Expect = 2.8
Identities = 16/62 (25%), Positives = 28/62 (45%)
Query: 31 KNKENSSVEMNMSNFNSSNSMSSSDLNKSRGNEERKRSQSVGRKTPKTPKKSPGRHKSNP 90
K+ + E + +N N SN+ + + N S N E+K S ++ + PK P + P
Sbjct: 49 IPKKPDNKEPSENNNNKSNNENKDEENPSSTNPEKKPDPSKNKEEIEKPKDEPKKPDKKP 108
Query: 91 NT 92
Sbjct: 109 QA 110
>gnl|CDD|178752 PLN03213, PLN03213, repressor of silencing 3; Provisional.
Length = 759
Score = 30.6 bits (68), Expect = 2.9
Identities = 25/94 (26%), Positives = 41/94 (43%), Gaps = 7/94 (7%)
Query: 8 NDLNSALNMDEPLTKGPLPRWQRKNKENSSVEMNMSNFNSSNSMSSSDLNKSRGNEERKR 67
N +NS +N + +E++ +E + N + + S +D++ + RKR
Sbjct: 192 NVMNSVMNKLFEKNNIDIA------EEDNEIEADQDNLIINVASSGNDMDSALDKLSRKR 245
Query: 68 SQSVGRKTPKTPKKSPGRHKSNPNTPSAKSKTPS 101
+ KTP S GR K N PS K +T S
Sbjct: 246 KSILNEKTPSEEGYSEGR-KGNHIHPSKKRQTIS 278
>gnl|CDD|218941 pfam06217, GAGA_bind, GAGA binding protein-like family. This
family includes gbp a protein from Soybean that binds to
GAGA element dinucleotide repeat DNA. It seems likely
that the this domain mediates DNA binding. This putative
domain contains several conserved cysteines and a
histidine suggesting this may be a zinc-binding DNA
interaction domain.
Length = 301
Score = 29.9 bits (67), Expect = 4.2
Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 1/54 (1%)
Query: 62 NEERKRSQSVGRKTPKTPKKS-PGRHKSNPNTPSAKSKTPSGGDRYIPNRSAID 114
E ++ + ++PK PK P + K + + K P R P+ + D
Sbjct: 142 PEAKEVKKPKKGQSPKVPKAPKPKKPKKKGSVSNRSVKMPGIDPRSKPDWKSQD 195
>gnl|CDD|226096 COG3566, COG3566, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 379
Score = 29.9 bits (67), Expect = 4.5
Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 2/58 (3%)
Query: 94 SAKSKTPSGGDRYIPNRSAIDTELSHYLLTRDE-NMEDLSPSEREKR-KAMSELVHGK 149
+A++K SG A ELS L + N D P +R+ +A + L+
Sbjct: 230 AAQAKLDSGQALTKEELDAKKAELSKALAALEAANAADEDPQDRDAAVEAAARLMGAA 287
>gnl|CDD|236792 PRK10905, PRK10905, cell division protein DamX; Validated.
Length = 328
Score = 29.5 bits (66), Expect = 5.3
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 64 ERKRSQSVGRKTPKTPKKSPGRHKSNPNTPSAKSKTP 100
E K+ Q+ + PK ++P R + P P A +K P
Sbjct: 164 EPKKPQATAKTEPKPVAQTPKR--TEPAAPVASTKAP 198
>gnl|CDD|236273 PRK08477, PRK08477, biotin--protein ligase; Provisional.
Length = 211
Score = 28.4 bits (64), Expect = 8.3
Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 558 LNLAMSPDETTVLSAGADETLRLWKIFEKVKSKKKEIKNNASKF 601
LNL SP L + L L +K++ KK K SK+
Sbjct: 126 LNLKFSPKNFACLDIEISDDLLLEGFLQKIE-KKILWKQIFSKY 168
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 29.0 bits (65), Expect = 8.7
Identities = 16/80 (20%), Positives = 27/80 (33%), Gaps = 1/80 (1%)
Query: 23 GPLPRWQRKNKENSSVEMNMSNFNSSNSMSSSDLNKSRGNEERKRSQSVGRKTPKTPKKS 82
P + + + +SS+S S + + + E R +V + S
Sbjct: 293 ERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPS 352
Query: 83 PGRHKSNPNTPSAKSKTPSG 102
P R P PS+ K P
Sbjct: 353 PSRPPP-PADPSSPRKRPRP 371
>gnl|CDD|183831 PRK12933, secD, preprotein translocase subunit SecD; Reviewed.
Length = 604
Score = 28.9 bits (65), Expect = 9.4
Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 17/66 (25%)
Query: 547 VAELHGHSARVLNLAMSPDETTVLSAGADETLRLWKIFEKVKSKKKEIKNNASK----FN 602
V L G + VL + M+ D T VL IFE++K K KE ++ A F+
Sbjct: 490 VLTLPGIAGLVLTVGMAVD-TNVL------------IFERIKDKLKEGRSFAQAIDTGFD 536
Query: 603 SMFNSI 608
S F++I
Sbjct: 537 SAFSTI 542
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
0.315 0.129 0.390
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: 29,715,562
Number of extensions: 2766542
Number of successful extensions: 2437
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2367
Number of HSP's successfully gapped: 60
Length of query: 609
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 506
Effective length of database: 6,369,140
Effective search space: 3222784840
Effective search space used: 3222784840
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)