RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1424
(305 letters)
>gnl|CDD|217519 pfam03371, PRP38, PRP38 family. Members of this family are related
to the pre mRNA splicing factor PRP38 from yeast.
Therefore all the members of this family could be
involved in splicing. This conserved region could be
involved in RNA binding. The putative domain is about
180 amino acids in length. PRP38 is a unique component
of the U4/U6.U5 tri-small nuclear ribonucleoprotein
(snRNP) particle and is necessary for an essential step
late in spliceosome maturation.
Length = 173
Score = 260 bits (668), Expect = 2e-88
Identities = 96/172 (55%), Positives = 128/172 (74%), Gaps = 1/172 (0%)
Query: 7 KDAKSVRGTNPQYLIEKIIRARIYDSKYWKEECFALSAELLVDKAME-LRYIGGVFGGNI 65
A + GTNP LIEKIIR RIYDS Y+KE F L+AE +VD+ +E + +IGG +GGN
Sbjct: 2 SGADKLNGTNPTLLIEKIIRDRIYDSPYYKENLFGLNAETIVDEIVEIVDHIGGTYGGNR 61
Query: 66 KPTPFLCLILKMLQIQPEKDIVVEFIKNEEFKYVRALGAYYMRLTGSSVDCYKYLEPLFA 125
+P+PFLCL+LK+LQIQP K+I+ E + NE+FKY+RALG +Y+RLT D YK+LEP
Sbjct: 62 RPSPFLCLLLKLLQIQPSKEIIKELLNNEDFKYIRALGLFYLRLTYPPADLYKWLEPYLQ 121
Query: 126 DSRKLRFQNRQGAFEVIHMDEYIDQLLREERMCDVILPRIQKRHVLEENNEI 177
D RKLR + G F++ HMDE++D LL ++R+CD ILPRI KR +LEE+ E+
Sbjct: 122 DYRKLRPKLGDGDFKLTHMDEFVDDLLTKDRVCDTILPRIPKRIILEEDGEL 173
>gnl|CDD|233503 TIGR01642, U2AF_lg, 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.
Length = 509
Score = 54.9 bits (132), Expect = 2e-08
Identities = 32/86 (37%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 227 RDPDKERDR-RYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDY----- 280
R+ +K R R R RS + + R R+RSR ++R RR R +S R R DR RY
Sbjct: 7 REREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSL 66
Query: 281 EREKYRSDRDRGDRRDRG-DRDRRHR 305
R RDR RR R +HR
Sbjct: 67 RYSSVRRSRDRPRRRSRSVRSIEQHR 92
Score = 44.1 bits (104), Expect = 6e-05
Identities = 28/88 (31%), Positives = 37/88 (42%), Gaps = 18/88 (20%)
Query: 227 RDPDKERDR-RYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKD------ 279
D ++E+ R R R S + R R R RS+ RDR RS+ +R +D
Sbjct: 5 PDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSR---------ERSYREDSRPRDR 55
Query: 280 --YEREKYRSDRDRGDRRDRGDRDRRHR 305
Y+ RS R RR R RR R
Sbjct: 56 RRYDSRSPRSLRYSSVRRSRDRPRRRSR 83
Score = 43.0 bits (101), Expect = 1e-04
Identities = 24/63 (38%), Positives = 30/63 (47%), Gaps = 4/63 (6%)
Query: 244 KERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKD---YEREKYRSDRDRGDRRDRGDR 300
+E RER +S+ RDR S+ PR + RD R R + ER R R DRR R
Sbjct: 3 EEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPR-DRRRYDSR 61
Query: 301 DRR 303
R
Sbjct: 62 SPR 64
Score = 41.8 bits (98), Expect = 3e-04
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 4/62 (6%)
Query: 244 KERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSDRDRGDRRDRGDRDRR 303
++ +R R K R R S R + R DR R R+++R R+R R D RDRR
Sbjct: 1 RDEEPDREREKSRGRDRDRSSERPRRRSRDRSR----FRDRHRRSRERSYREDSRPRDRR 56
Query: 304 HR 305
Sbjct: 57 RY 58
Score = 39.9 bits (93), Expect = 0.001
Identities = 27/98 (27%), Positives = 41/98 (41%), Gaps = 8/98 (8%)
Query: 209 KNRMDVDTYHSSKYDSHHRDPDKERDR---RYRSEKSTKERVRERSRSKERDRRHRSKSP 265
+R + + S R + RDR R R +S + RE SR ++R RR+ S+SP
Sbjct: 5 PDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDR-RRYDSRSP 63
Query: 266 RHKDRD-YDRDRYKDYEREKYRSDRDRGDRRDRGDRDR 302
R R R + R + ++ R RDR
Sbjct: 64 RSLRYSSVRRSRDRPRRRSR---SVRSIEQHRRRLRDR 98
Score = 37.6 bits (87), Expect = 0.007
Identities = 27/106 (25%), Positives = 40/106 (37%), Gaps = 10/106 (9%)
Query: 190 DGGSSSSEDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPDKERDRRYRSEKST---KER 246
D SS ++R S + DS RD + R RS + + + R
Sbjct: 16 DRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSR 75
Query: 247 VRERSRSKERD------RRHRSKSPRHKDRDYDRDR-YKDYEREKY 285
R R RS+ RR R +SP ++ R D+ R D + Y
Sbjct: 76 DRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLWDIKPPGY 121
Score = 35.6 bits (82), Expect = 0.031
Identities = 24/107 (22%), Positives = 37/107 (34%), Gaps = 3/107 (2%)
Query: 197 EDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPDKE-RDRRYRSEKSTKERVRERSRSKE 255
D E D++R S+ S RD + R+R YR + ++R R SRS
Sbjct: 5 PDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPR 64
Query: 256 RDRRHRSKSPRHKD--RDYDRDRYKDYEREKYRSDRDRGDRRDRGDR 300
R + R + R + + R R+D R
Sbjct: 65 SLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKR 111
>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 = 51.8 bits (124), Expect = 2e-07
Identities = 32/80 (40%), Positives = 41/80 (51%), Gaps = 6/80 (7%)
Query: 227 RDPDKERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDR-YKDYEREKY 285
R D+ER R R++ ++ RERSR + R R +S R +DRDY R R + R
Sbjct: 1 RYRDRER-GRLRNDTRRSDKGRERSRRRSRSRD---RSRRRRDRDYYRGRRGRSRSRSPN 56
Query: 286 RSDRDRGDRRDRGDRDRRHR 305
R R RGDR R DRR
Sbjct: 57 RYYRPRGDRSYR-RDDRRSG 75
Score = 41.4 bits (97), Expect = 4e-04
Identities = 26/88 (29%), Positives = 40/88 (45%), Gaps = 5/88 (5%)
Query: 220 SKYDSHHRDPDKERDR-RYRSEKSTKER---VRERSRSKERDRRHRSKSPRHKDRDYDRD 275
+ R+ + D+ R RS + ++ R R R R R RR RS+S R +R Y
Sbjct: 4 DRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRS-RSPNRYYRPR 62
Query: 276 RYKDYEREKYRSDRDRGDRRDRGDRDRR 303
+ Y R+ RS R+ + +RD R
Sbjct: 63 GDRSYRRDDRRSGRNTKEPLTEAERDDR 90
>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 45.7 bits (109), Expect = 2e-05
Identities = 25/121 (20%), Positives = 35/121 (28%), Gaps = 5/121 (4%)
Query: 185 DDDIDDGGSSSSEDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPDKERDRRYRSEKSTK 244
+ D + E+ +E ++R +RDRR R E+
Sbjct: 155 EARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQG-- 212
Query: 245 ERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSDRDRGDRRDRGDRDRRH 304
R RD R R +DR R +R D G RG R R
Sbjct: 213 ---DRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDR 269
Query: 305 R 305
Sbjct: 270 D 270
Score = 44.1 bits (105), Expect = 7e-05
Identities = 23/119 (19%), Positives = 41/119 (34%), Gaps = 17/119 (14%)
Query: 185 DDDIDDGGSSSSEDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPDKERDRRYRSEKSTK 244
+ + G E+ + + ++R + D +ER RR ++ +
Sbjct: 182 QAEAERGERGRREERGRDGDDRDRRDRRE------------QGDRREERGRRDGGDRRGR 229
Query: 245 ERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSDRDRGDRRDRGDRDRR 303
R R+R ++ D R D + R R + DRDR RR + R
Sbjct: 230 RRRRDRRDARGDDNREDRGDRDGDDGEGRGGR-----RGRRFRDRDRRGRRGGDGGNER 283
Score = 42.6 bits (101), Expect = 2e-04
Identities = 21/81 (25%), Positives = 29/81 (35%), Gaps = 1/81 (1%)
Query: 226 HRDPDKERDRRYRSEKSTKERVRERSRSKERDR-RHRSKSPRHKDRDYDRDRYKDYEREK 284
RD D R R + +E R R R R R + D + + +D + +
Sbjct: 197 GRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGE 256
Query: 285 YRSDRDRGDRRDRGDRDRRHR 305
R R RDR R RR
Sbjct: 257 GRGGRRGRRFRDRDRRGRRGG 277
Score = 38.3 bits (90), Expect = 0.004
Identities = 14/77 (18%), Positives = 25/77 (32%), Gaps = 1/77 (1%)
Query: 227 RDPDKERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYR 286
R E RR + K+ + + + ++ + R + R DR +
Sbjct: 130 RRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRR-RGDREDRQAEAERG 188
Query: 287 SDRDRGDRRDRGDRDRR 303
R +R GD R
Sbjct: 189 ERGRREERGRDGDDRDR 205
Score = 38.3 bits (90), Expect = 0.004
Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 3/80 (3%)
Query: 227 RDPDKERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYR 286
+ R +E++ +E ER R +R+ R + R +R R D + R
Sbjct: 149 GEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGR--DGDDRDRR 206
Query: 287 SDRDRGDRR-DRGDRDRRHR 305
R++GDRR +RG RD R
Sbjct: 207 DRREQGDRREERGRRDGGDR 226
Score = 38.0 bits (89), Expect = 0.006
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 1/77 (1%)
Query: 227 RDPDKERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYR 286
R ++ +T+ R R++E +R R + +DR + +R + RE+
Sbjct: 139 RGAARKAGEGGEQP-ATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERG 197
Query: 287 SDRDRGDRRDRGDRDRR 303
D D DRRDR ++ R
Sbjct: 198 RDGDDRDRRDRREQGDR 214
Score = 37.6 bits (88), Expect = 0.007
Identities = 18/78 (23%), Positives = 31/78 (39%), Gaps = 5/78 (6%)
Query: 228 DPDKERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRS 287
+ R R E+ R ++ E + P + R +R ++ ER++ R
Sbjct: 120 SAPEAAQARERRERGEAARRGAARKAGEGGEQ-----PATEARADAAERTEEEERDERRR 174
Query: 288 DRDRGDRRDRGDRDRRHR 305
DR DR+ +R R R
Sbjct: 175 RGDREDRQAEAERGERGR 192
Score = 37.2 bits (87), Expect = 0.010
Identities = 25/131 (19%), Positives = 42/131 (32%), Gaps = 11/131 (8%)
Query: 185 DDDIDDGGSSSSEDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPDKERDRRYRSEKSTK 244
+ + E EA + + E + R +
Sbjct: 118 AASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEER-DERRRRG 176
Query: 245 ERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSDRDRGDR---------- 294
+R ++ ++ +R R + R D RDR + +R + R RD GDR
Sbjct: 177 DREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRR 236
Query: 295 RDRGDRDRRHR 305
RGD +R R
Sbjct: 237 DARGDDNREDR 247
>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777). This is
a family of eukaryotic proteins of unknown function.
Some of the proteins in this family are putative nucleic
acid binding proteins.
Length = 158
Score = 36.8 bits (85), Expect = 0.004
Identities = 32/80 (40%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 224 SHHRDPDKERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYERE 283
S R P + R R + +ER RERSRS+ERDRR RS+S R R R
Sbjct: 4 SRSRSPRRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSP--HRSRRSRSPRRHRS 61
Query: 284 KYRSDRDRGDRRDRGDRDRR 303
+ RS R DR+ D+D R
Sbjct: 62 RSRSPSRRRDRKRERDKDAR 81
Score = 30.2 bits (68), Expect = 0.84
Identities = 27/87 (31%), Positives = 38/87 (43%), Gaps = 6/87 (6%)
Query: 216 TYHSSKYDSHHRDPDKERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRD 275
+ S+ R D+ RR RS ++R R RSRS+ R RS+SPR R
Sbjct: 8 SPRRSRRRGRSRSRDRRERRRERSRSRERDRRR-RSRSRSPHRSRRSRSPRR-----HRS 61
Query: 276 RYKDYEREKYRSDRDRGDRRDRGDRDR 302
R + R + R D R+ R+R
Sbjct: 62 RSRSPSRRRDRKRERDKDAREPKKRER 88
Score = 29.5 bits (66), Expect = 1.4
Identities = 22/59 (37%), Positives = 27/59 (45%), Gaps = 7/59 (11%)
Query: 248 RERSRSKERDRRHRSKSPRHKDRDY---DRDRYKDYEREKYRSDRDRGDRRDRGDRDRR 303
R RSRS R RR R + RD R+R + ER++ R R R R R R R
Sbjct: 3 RSRSRSPRRSRRR----GRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPR 57
>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed.
Length = 1068
Score = 35.0 bits (81), Expect = 0.044
Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 3/71 (4%)
Query: 233 RDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSDRDRG 292
RDR R + RE ++E +RR+R ++ + + + + E+ + +D
Sbjct: 615 RDRNERRDTRDNRTRREGRENREENRRNRRQAQQQTAETRESQQAEVTEKAR---TQDEQ 671
Query: 293 DRRDRGDRDRR 303
+ R +R RR
Sbjct: 672 QQAPRRERQRR 682
Score = 32.7 bits (75), Expect = 0.23
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 6/67 (8%)
Query: 239 SEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSDRDRGDRRDRG 298
E++ + + +R+ + PR +R RDR ER R +R R + R+
Sbjct: 583 GEETKPQEQPAPKAEAKPERQQDRRKPRQNNR---RDRN---ERRDTRDNRTRREGRENR 636
Query: 299 DRDRRHR 305
+ +RR+R
Sbjct: 637 EENRRNR 643
>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional.
Length = 1021
Score = 34.7 bits (79), Expect = 0.059
Identities = 26/84 (30%), Positives = 38/84 (45%), Gaps = 8/84 (9%)
Query: 230 DKERDRRYRSEKSTKERV--------RERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYE 281
DK+ R R EK R ++R ER+ R R + R + + +R + E
Sbjct: 431 DKDHAERARIEKENAHRKALEMKILEKKRIERLEREERERLERERMERIERERLERERLE 490
Query: 282 REKYRSDRDRGDRRDRGDRDRRHR 305
RE+ DR DR DR +R+R R
Sbjct: 491 RERLERDRLERDRLDRLERERVDR 514
Score = 34.3 bits (78), Expect = 0.081
Identities = 29/96 (30%), Positives = 46/96 (47%), Gaps = 4/96 (4%)
Query: 214 VDTYHSSKYDSHHRDP---DKERDRRYRSEKSTKERVR-ERSRSKERDRRHRSKSPRHKD 269
V+ ++ + D H + +KE R E E+ R ER +ER+R R + R +
Sbjct: 422 VNGHYGGRVDKDHAERARIEKENAHRKALEMKILEKKRIERLEREERERLERERMERIER 481
Query: 270 RDYDRDRYKDYEREKYRSDRDRGDRRDRGDRDRRHR 305
+R+R + E+ R +RDR DR +R DR R
Sbjct: 482 ERLERERLERERLERDRLERDRLDRLERERVDRLER 517
Score = 32.8 bits (74), Expect = 0.23
Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 9/72 (12%)
Query: 232 ERDRRYRSEKSTKERV-RERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSDRD 290
E+ R R E+ +ER+ RER ER+R R + +R+R + E+ R DR
Sbjct: 456 EKKRIERLEREERERLERERMERIERERLERER--------LERERLERDRLERDRLDRL 507
Query: 291 RGDRRDRGDRDR 302
+R DR +RDR
Sbjct: 508 ERERVDRLERDR 519
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 33.5 bits (76), Expect = 0.14
Identities = 13/40 (32%), Positives = 23/40 (57%)
Query: 231 KERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDR 270
+++ R R + KE+ RER R +E +R ++ S H+ R
Sbjct: 593 EQKAREEREREKEKEKEREREREREAERAAKASSSSHESR 632
Score = 32.4 bits (73), Expect = 0.30
Identities = 13/40 (32%), Positives = 24/40 (60%)
Query: 227 RDPDKERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPR 266
R+ E+ +R +K+ +ER RE+ + KER+R ++ R
Sbjct: 581 REEAVEKAKREAEQKAREEREREKEKEKEREREREREAER 620
>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein. CDC45 is an essential gene
required for initiation of DNA replication in S.
cerevisiae, forming a complex with MCM5/CDC46.
Homologues of CDC45 have been identified in human, mouse
and smut fungus among others.
Length = 583
Score = 31.9 bits (73), Expect = 0.47
Identities = 18/101 (17%), Positives = 26/101 (25%), Gaps = 23/101 (22%)
Query: 172 EENNEIEVKVSILDDDIDDGGSSSSEDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPDK 231
EE + D +D DE +E S + D D
Sbjct: 108 EELQDEPRYDDAYRDLEEDDDDDEESDEEDEESS------------KSEDDEDDDDDDDD 155
Query: 232 ERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDY 272
+ RERS + R RR + + Y
Sbjct: 156 DDIAT-----------RERSLERRRRRREWEEKRAELEFYY 185
>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3. This
protein, which interacts with both microtubules and
TRAF3 (tumour necrosis factor receptor-associated factor
3), is conserved from worms to humans. The N-terminal
region is the microtubule binding domain and is
well-conserved; the C-terminal 100 residues, also
well-conserved, constitute the coiled-coil region which
binds to TRAF3. The central region of the protein is
rich in lysine and glutamic acid and carries KKE motifs
which may also be necessary for tubulin-binding, but
this region is the least well-conserved.
Length = 506
Score = 31.8 bits (72), Expect = 0.50
Identities = 13/79 (16%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 227 RDPDKERDRRYRSEKSTKERVRERSRSKERDR--RHRSKSPRHKDRDYDRDRYKDYEREK 284
+ KE+ + ++ KE +E+ KE+++ + + PR ++ + R+R + R K
Sbjct: 117 KKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPK 176
Query: 285 YRSDRDRGDR-RDRGDRDR 302
+ ++ ++ + ++
Sbjct: 177 KPPKKKPPNKKKEPPEEEK 195
>gnl|CDD|227742 COG5455, COG5455, Predicted integral membrane protein [Function
unknown].
Length = 129
Score = 30.2 bits (68), Expect = 0.57
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 251 SRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKY--RSDRDRGDRRDRGDR 300
+R + RH DRD DR + ER Y +S + +R RGDR
Sbjct: 25 DGEFMDIKRKMPQGARHLDRDRAWDRPRTVERRSYELKSVIAKFNRWKRGDR 76
>gnl|CDD|219406 pfam07420, DUF1509, Protein of unknown function (DUF1509). This
family consists of several uncharacterized viral
proteins from the Marek's disease-like viruses. Members
of this family are typically around 400 residues in
length. The function of this family is unknown.
Length = 377
Score = 30.8 bits (69), Expect = 0.84
Identities = 14/42 (33%), Positives = 17/42 (40%)
Query: 234 DRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRD 275
+RR R ++ R R RSRS R R R R R
Sbjct: 324 ERRGRRRNRSESRSRSRSRSGSRRYRRRRGRGVPGRRSESRQ 365
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 31.0 bits (70), Expect = 0.89
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 274 RDRYKDYEREKYRSDRDRGDRRDRGDRDRRHR 305
+ ++D + R DRG R DR DR RR R
Sbjct: 449 KREFRDRDDRGPRDRNDRGPRGDREDRPRRER 480
>gnl|CDD|184287 PRK13735, PRK13735, conjugal transfer mating pair stabilization
protein TraG; Provisional.
Length = 942
Score = 30.9 bits (70), Expect = 1.0
Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 2/82 (2%)
Query: 187 DIDDGGSSSSEDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPDKERDRRYRSEKSTKER 246
+D+ + + + + V S+ +HH+ ++ +Y EKS +ER
Sbjct: 862 QVDNMVTEYEGNIGDTQNSI-RGEENTVKG-QYSELQNHHKTEALSQNNKYNEEKSAQER 919
Query: 247 VRERSRSKERDRRHRSKSPRHK 268
+ +E +R + +HK
Sbjct: 920 MPGADSPEELMKRAKEYQDKHK 941
>gnl|CDD|236779 PRK10864, PRK10864, putative methyltransferase; Provisional.
Length = 346
Score = 30.5 bits (69), Expect = 1.1
Identities = 15/61 (24%), Positives = 19/61 (31%), Gaps = 1/61 (1%)
Query: 241 KSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSDRDRGDRRDRGDR 300
KS K +V + D+R + D R R DR RDR
Sbjct: 8 KSGKVKVMYVRSDDDSDKRTHNPRTGKGGGRPSGKSRADGGRRPARDDR-NSQSRDRKWE 66
Query: 301 D 301
D
Sbjct: 67 D 67
Score = 29.7 bits (67), Expect = 1.8
Identities = 9/49 (18%), Positives = 13/49 (26%)
Query: 238 RSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYR 286
RS+ + +R K R R DR K+
Sbjct: 18 RSDDDSDKRTHNPRTGKGGGRPSGKSRADGGRRPARDDRNSQSRDRKWE 66
>gnl|CDD|165391 PHA03118, PHA03118, multifunctional expression regulator;
Provisional.
Length = 474
Score = 30.4 bits (68), Expect = 1.2
Identities = 25/132 (18%), Positives = 35/132 (26%), Gaps = 11/132 (8%)
Query: 176 EIEVKVSILDDDIDDGGSSSSEDEN--------EEAGEVYDKNRMDVDTYHSSKYDSHHR 227
E V S+ DD + G EDE E+A Y + H + HH
Sbjct: 42 EESVPNSVQIDDDEAAGEILGEDEETPNPADVCEDADRAYTNPNFE-KKAHGRREGYHHD 100
Query: 228 DPDKERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKY-- 285
D E R KS + R RD + +
Sbjct: 101 DEKCLVTFLDDINHHGGRDTEPGHAHIENGERKSPKSYNQQSRKKHRDESLRNKHGRPSG 160
Query: 286 RSDRDRGDRRDR 297
G+ D+
Sbjct: 161 PPAMSPGEHFDQ 172
>gnl|CDD|219061 pfam06495, Transformer, Fruit fly transformer protein. This family
consists of transformer proteins from several Drosophila
species and also from Ceratitis capitata (Mediterranean
fruit fly). The transformer locus (tra) produces an RNA
processing protein that alternatively splices the
doublesex pre-mRNA in the sex determination hierarchy of
Drosophila melanogaster.
Length = 182
Score = 29.6 bits (66), Expect = 1.2
Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 13/77 (16%)
Query: 227 RDPDKERDRRYRSEKSTKE---------RVRERSRSKERDRRHRSKSPRHKDRDYDRDRY 277
R+ D+ R+ R R +ST+ R R RS+S ER+ R RH+ R R+R
Sbjct: 31 RERDRVRNLRQRKTQSTRPTTSHRGRRTRSRSRSQSAERNSCQR----RHRSRSRSRNRS 86
Query: 278 KDYEREKYRSDRDRGDR 294
R ++R R R
Sbjct: 87 DSRHRSTSSTERRRRSR 103
>gnl|CDD|177566 PHA03242, PHA03242, envelope glycoprotein M; Provisional.
Length = 428
Score = 30.2 bits (68), Expect = 1.4
Identities = 17/72 (23%), Positives = 25/72 (34%), Gaps = 7/72 (9%)
Query: 225 HHRDPDKERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDR---YKDYE 281
+HR + R R Y + + R R R R+ ++P + D RD D E
Sbjct: 350 YHR---RHRSRFYGHVRDARHRARSYIRRVRSSMRNSREAPYAGESDVGRDDDYASTDGE 406
Query: 282 REKYRSDRDRGD 293
Y D
Sbjct: 407 PI-YDEVAPDED 417
>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen. The core
antigen of hepatitis viruses possesses a carboxyl
terminus rich in arginine. On this basis it was
predicted that the core antigen would bind DNA. There is
some experimental evidence to support this.
Length = 182
Score = 29.4 bits (66), Expect = 1.5
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 233 RDRRYRSEKSTKERVRERSRSKERDRRHRSKSPR 266
R R + T R RS+S R RR +S S +
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRR-RRSQSPSSQ 181
>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated
hydrophilic C-term. This domain is a hydrophilic region
found at the C-terminus of plant and metazoan
pre-mRNA-splicing factor 38 proteins. The function is
not known.
Length = 97
Score = 28.2 bits (63), Expect = 1.7
Identities = 22/76 (28%), Positives = 30/76 (39%)
Query: 227 RDPDKERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYR 286
++E D R + RS + RR R + K R RDR + R++
Sbjct: 15 ESEEEEDDEEIRRKAERDVDRGRRSPRRRTRRRSRRRKRSRKRRRRRRDRDRARYRDRDD 74
Query: 287 SDRDRGDRRDRGDRDR 302
DRDR DR R R
Sbjct: 75 RDRDRYDRSRSRSRSR 90
>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase
component YidC; Validated.
Length = 429
Score = 29.0 bits (65), Expect = 2.9
Identities = 15/88 (17%), Positives = 29/88 (32%), Gaps = 6/88 (6%)
Query: 222 YDSHHRDPDKERDRRYRS---EKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYK 278
++ E+ +YR EK R+R + R+ ++ + + R
Sbjct: 279 LTDEFKEHHAEQRAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAENAEIKKTRTA 338
Query: 279 DYEREKYRSDRDRGDRR---DRGDRDRR 303
+ K R RR +R+ R
Sbjct: 339 EKNEAKARKKEIAQKRRAAEREINREAR 366
Score = 27.5 bits (61), Expect = 9.6
Identities = 13/76 (17%), Positives = 32/76 (42%)
Query: 209 KNRMDVDTYHSSKYDSHHRDPDKERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHK 268
+ RM + + + + + + + K R K+ K+ + ++ R+ ER+ ++ R
Sbjct: 312 RLRMIITPWRAPELHAENAEIKKTRTAEKNEAKARKKEIAQKRRAAEREINREARQERAA 371
Query: 269 DRDYDRDRYKDYEREK 284
R R + +K
Sbjct: 372 AMARARARRAAVKAKK 387
>gnl|CDD|132514 TIGR03474, incFII_RepA, incFII family plasmid replication initiator
RepA. Members of this protein are the plasmid
replication initiator RepA of incFII (plasmid
incompatibility group F-II) plasmids. R1 and R100 are
plasmids in this group. Immediately upstream of repA is
found tap, a leader peptide of about 24 amino acids,
often not assigned as a gene in annotated plasmid
sequences. Note that other, non-homologous plasmid
replication proteins share the gene symbol (repA) and
similar names (plasmid replication protein RepA).
Length = 275
Score = 28.8 bits (64), Expect = 3.1
Identities = 18/59 (30%), Positives = 27/59 (45%)
Query: 247 VRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSDRDRGDRRDRGDRDRRHR 305
VRER RS + +R+ RD DR+R K + R+ + R G+R+ R
Sbjct: 193 VRERFRSYQTERKSHGIKRARARRDADRERQDIETLVKRQLTREIAEGRFTGNREAVKR 251
>gnl|CDD|184300 PRK13750, PRK13750, replication protein; Provisional.
Length = 285
Score = 28.7 bits (64), Expect = 3.1
Identities = 17/59 (28%), Positives = 26/59 (44%)
Query: 247 VRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSDRDRGDRRDRGDRDRRHR 305
VRER RS + + + R RD DR+R K + R+ + R +R+ R
Sbjct: 201 VRERFRSYQTELKSRGIKRARARRDADRERQDIVTLVKRQLTREIAEGRFTANREAVKR 259
>gnl|CDD|224415 COG1498, SIK1, Protein implicated in ribosomal biogenesis, Nop56p
homolog [Translation, ribosomal structure and
biogenesis].
Length = 395
Score = 28.9 bits (65), Expect = 3.2
Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 10/78 (12%)
Query: 219 SSKYDSHHRDPDKERDRRYRSEKSTKERVRERSRS-KERDRRHRSKSPRHKDRDYDRDRY 277
+++ D+ +PD S +E + +R KE+ + +K+ +D+ RY
Sbjct: 327 AARIDAFSGEPDGI---------SLREELEKRIEKLKEKPPKPPTKAKPERDKKERPGRY 377
Query: 278 KDYEREKYRSDRDRGDRR 295
+ ++EK RG +
Sbjct: 378 RRKKKEKKAKSERRGLQN 395
>gnl|CDD|163244 TIGR03385, CoA_CoA_reduc, CoA-disulfide reductase. Members of this
protein family are CoA-disulfide reductase (EC
1.8.1.14), as characterized in Staphylococcus aureus,
Pyrococcus horikoshii, and Borrelia burgdorferi, and
inferred in several other species on the basis of high
levels of CoA and an absence of glutathione as a
protective thiol [Cellular processes, Detoxification].
Length = 427
Score = 28.6 bits (64), Expect = 4.4
Identities = 19/134 (14%), Positives = 40/134 (29%), Gaps = 33/134 (24%)
Query: 82 PEKDIVVEFIKNEEFKYVRALGAYYMRLTGSSVDCYKYLEPLFADSRKLRFQNRQGAFEV 141
+ D + ++I + + V +G Y+ + + E L + + +
Sbjct: 123 EDTDAIKQYIDKNKVENVVIIGGGYIGI--------EMAEALRERGKNVT---------L 165
Query: 142 IHMDEYIDQLLREERMCDVILPRIQKRHVLEENNEIEVKVSILDDDIDDGGSSSSEDENE 201
IH E I L +E M ++ ++K + NE + + E
Sbjct: 166 IHRSERILNKLFDEEMNQIVEEELKKHEINLRLNEEVDSI----------------EGEE 209
Query: 202 EAGEVYDKNRMDVD 215
D
Sbjct: 210 RVKVFTSGGVYQAD 223
>gnl|CDD|233877 TIGR02466, TIGR02466, conserved hypothetical protein. This family
consists of uncharacterized proteins in Caulobacter
crescentus CB15, Bdellovibrio bacteriovorus HD100,
Synechococcus sp. WH 8102 (2), Silicibacter pomeroyi
DSS-3 (2), and Hyphomonas neptunium ATCC 15444. The
context of nearby genes differs substantially between
members and does point to any specific biological role
[Hypothetical proteins, Conserved].
Length = 201
Score = 28.2 bits (63), Expect = 4.7
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 193 SSSSEDENEEAGEVY-DKNRMDVDTYHSSKYDSHHRDP 229
S S E++EAG+ + ++N + T ++S D HR P
Sbjct: 27 SLYSIAEDDEAGQEWSNRNGLGGYTSYASLLDLPHRFP 64
>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31;
Provisional.
Length = 316
Score = 28.5 bits (64), Expect = 5.0
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 6/61 (9%)
Query: 229 PDKERDRRYRSEKSTKERVRE---RSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKY 285
+ RS ++ + R+ SR + R R R S R R R D ER++Y
Sbjct: 6 LRRSSSSLRRSRRAARRSRRDGRVGSRGRSRYRSRRRSSRRSSTR---RAELADTERDRY 62
Query: 286 R 286
R
Sbjct: 63 R 63
>gnl|CDD|219668 pfam07964, Red1, Rec10 / Red1. Rec10 / Red1 is involved in meiotic
recombination and chromosome segregation during
homologous chromosome formation. This protein localises
to the synaptonemal complex in S. cerevisiae and the
analogous structures (linear elements) in S. pombe. This
family is currently only found in fungi.
Length = 706
Score = 28.3 bits (63), Expect = 6.1
Identities = 19/118 (16%), Positives = 39/118 (33%), Gaps = 2/118 (1%)
Query: 154 EERMCDVILPRIQK-RHVLEENNEIEVK-VSILDDDIDDGGSSSSEDENEEAGEVYDKNR 211
+E++ + L + E + + +D+I + E E D
Sbjct: 212 DEKLGETFLNASTNLPKISEVQAYLTLNFPESFEDEIIESSVQDEECSREANVPTQDIEA 271
Query: 212 MDVDTYHSSKYDSHHRDPDKERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKD 269
D+ H S D+H+ + + R KS ++E + + K K+
Sbjct: 272 NTKDSLHMSAQDNHYDNTQLQTPERSTKRKSPIWDLKEDQKESKIKSGTNLKLSSEKE 329
>gnl|CDD|152107 pfam11671, Apis_Csd, Complementary sex determiner protein. This
family of proteins represents the complementary sex
determiner in the honeybee. In the honeybee, the
mechanism of sex determination depends on the csd gene
which produces an SR-type protein. Males are homozygous
while females are homozygous for the csd gene.
Heterozygosity generates an active protein which
initiates female development.
Length = 146
Score = 27.4 bits (60), Expect = 6.2
Identities = 14/50 (28%), Positives = 25/50 (50%)
Query: 231 KERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDY 280
+ER+++ +++ RE SR + RDR R +S HK + +Y
Sbjct: 10 REREQKSYKNENSYREYRETSRERSRDRTERERSREHKIISSLSNLSNNY 59
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 28.5 bits (63), Expect = 6.7
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 160 VILPRIQKRHVLEENNEIEVKVSILDDDIDDGGSSSSEDENEEAGE 205
+I+ R + RH+ EE+ I DDD +D ++E++E E
Sbjct: 130 IIIKRRRARHLAEEDMSPRDNFVI-DDDDEDEDEDDDDEEDDEEEE 174
>gnl|CDD|185618 PTZ00438, PTZ00438, gamete antigen 27/25-like protein; Provisional.
Length = 374
Score = 27.7 bits (61), Expect = 8.5
Identities = 14/64 (21%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 174 NNEIEVKVSILDDDI---DDGGSSSSEDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPD 230
+NE +V++ L+ + ++ G+ E+E+E+ E+ + ++V + +D +
Sbjct: 83 DNENDVELEGLNIIVKNEEERGTQKEEEEDEDVEEIEEVEEVEVVEEEYDDDEDSEKDDE 142
Query: 231 KERD 234
KE D
Sbjct: 143 KESD 146
>gnl|CDD|217348 pfam03064, U79_P34, HSV U79 / HCMV P34. This family represents
herpes virus protein U79 and cytomegalovirus early
phosphoprotein P34 (UL112).
Length = 238
Score = 27.5 bits (61), Expect = 9.2
Identities = 22/122 (18%), Positives = 44/122 (36%), Gaps = 13/122 (10%)
Query: 177 IEVKVSILDDDIDDGGSSSSEDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPDKERDRR 236
+ + +I + G + ++ E+ + + D D H + K++++R
Sbjct: 120 VTHSKVAHEAEIRNLGDVKNAEKFEKECRALSRKKSD---------DEHRKRSGKQKEKR 170
Query: 237 YRSEKSTKERVRERSRSKERDRRHRSKSPRHKDR---DYDRDRYKDYEREKYRSDRDRGD 293
R E S K + R + +E+ R K P KD ++ R +
Sbjct: 171 -RVEDSQKHKEDRRKKQEEKRRNDEDKRPGGGGGSSGGQSGLSTKDEPPKEKRQKHHDPE 229
Query: 294 RR 295
RR
Sbjct: 230 RR 231
>gnl|CDD|202036 pfam01902, ATP_bind_4, ATP-binding region. This family of proteins
probably binds ATP. This domain is about 200 amino acids
long with a strongly conserved motif SGGKD at the N
terminus.In some members of this family , this domain is
associated with pfam01042.
Length = 220
Score = 27.4 bits (61), Expect = 9.4
Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 5/77 (6%)
Query: 36 KEECFALSAELLVDKAMELRYIGGVFGGNIKPTPFLCLILKMLQIQPEK---DIVVEFIK 92
K+ +AL L + +E+ Y+ + N + + L + ++Q E I+ + K
Sbjct: 11 KDSNYALYWAL--KEGIEVPYLVSMKSENEESYMYHEPNLHLTKLQAEALGIPIIKLYTK 68
Query: 93 NEEFKYVRALGAYYMRL 109
E+ K V L + L
Sbjct: 69 GEKEKEVEDLAGFLESL 85
>gnl|CDD|130366 TIGR01299, synapt_SV2, synaptic vesicle protein SV2. This model
describes a tightly conserved subfamily of the larger
family of sugar (and other) transporters described by
PFAM model pfam00083. Members of this subfamily include
closely related forms SV2A and SV2B of synaptic vesicle
protein from vertebrates and a more distantly related
homolog (below trusted cutoff) from Drosophila
melanogaster. Members are predicted to have two sets of
six transmembrane helices.
Length = 742
Score = 27.6 bits (61), Expect = 9.9
Identities = 18/99 (18%), Positives = 40/99 (40%), Gaps = 12/99 (12%)
Query: 185 DDDIDDGGSSSSEDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPDKERDRRYRSEKSTK 244
DD+ + SS + + ++E E+Y+ +Y R + +D ++ + K
Sbjct: 72 DDEEEGEASSDATEGHDEDDEIYE-----------GEYQGIPRAENGGKDEIM-ADGAPK 119
Query: 245 ERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYERE 283
VR+ + E ++ R D + +Y+ +E
Sbjct: 120 AGVRDELKDGEGPPGGEGEAERRADEEELAQQYELIIQE 158
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
0.318 0.137 0.394
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,210,630
Number of extensions: 1626441
Number of successful extensions: 2733
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2244
Number of HSP's successfully gapped: 177
Length of query: 305
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 208
Effective length of database: 6,635,264
Effective search space: 1380134912
Effective search space used: 1380134912
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 (21.7 bits)
S2: 59 (26.6 bits)