RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6771
(493 letters)
>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 263 bits (674), Expect = 2e-84
Identities = 114/362 (31%), Positives = 181/362 (50%), Gaps = 64/362 (17%)
Query: 143 WDSYYLELLMIAGLVAYIINFITGRNKNFKLATHWINTHRALLEDNFSLVGDDGKQEIEN 202
++ LE+L + L+ YI N+ G+ KN + A W TH+ +LE NF+LVG DGK++
Sbjct: 1 PRNFRLEILFLGLLILYIANYFIGKRKNKRKALAWFKTHKPILESNFALVGFDGKED--- 57
Query: 203 SSLIKESENTFTLWCSGRDDGKQEIENSSLIKESENTFTLWCSGRSCCEGMLVELKLIKR 262
L++ES + F+ + +GR+ C G+LV LKL KR
Sbjct: 58 --------------------------EPILLEESPSEFSFYATGRTNCAGLLVNLKLKKR 91
Query: 263 QDLVGLIAQLIRP----STDQLSMSFDLGKEDMDSF--------------------SLYC 298
QDL+ L+ + + P D ++++ + E MD+F SL+
Sbjct: 92 QDLLSLLLEYVLPFFFAPKDTVTITIYMNNETMDNFVFAVVNKKAMKKFRKDNYDLSLFT 151
Query: 299 PERKSGDKFNLPSGFNVMSEIAEVSSSLIDSKFLTIVNKFSDLIDYIHISDQFSGPKQTE 358
K+ DK LP VMSE EV+ L+ + + +NK ++YIH +DQ G +T+
Sbjct: 152 ---KTSDKPKLPESLVVMSESNEVTDLLLTPELIQALNKAGKYLEYIHFTDQPVGKPETD 208
Query: 359 ETTLTKLPDVKKVILFNFNLQMGQLSIQDTIDEMKPLMQFVFYTLDRVKRFRLSREAKSK 418
K KK ++ +FNL ++ ++++ PL+ V Y +D++ +LS E K
Sbjct: 209 L----KETKPKKRLIISFNLP----KSKEDLEDLLPLLNLVLYLVDKLANLKLSPEVLRK 260
Query: 419 ADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEEKEAKRQM 478
DK R EE LK R E A +KEEK++ E+E + + PE+QR+ EEKE K+Q
Sbjct: 261 VDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEEKERKKQA 320
Query: 479 KK 480
+K
Sbjct: 321 RK 322
>gnl|CDD|220972 pfam11081, DUF2890, Protein of unknown function (DUF2890). This
family is conserved in dsDNA adenoviruses of
vertebrates. The function is not known.
Length = 172
Score = 38.4 bits (89), Expect = 0.003
Identities = 25/87 (28%), Positives = 39/87 (44%), Gaps = 7/87 (8%)
Query: 65 LKESLNVQQNVQETWEEEPVEAITEEDVMIEDEEDS-DFEHFKDEEEFEGFKTAKPDPTS 123
LK ++ +E W+ + E + E++ +ED EDS D E + EE E + P+S
Sbjct: 10 LKVRPPPTKDEEEDWDSQ-AEEVEEDEEEMEDWEDSLDEEDEEAEEVEEETAASSKAPSS 68
Query: 124 KQ---EAPTITIQDIPMHLRSN--WDS 145
TI+I P R + WD
Sbjct: 69 SSKSSSQETISIPPTPPARRPSRRWDQ 95
>gnl|CDD|206063 pfam13892, DBINO, DNA-binding domain. DBINO is a DNA-binding
domain found on global transcription activator SNF2L1
proteins and chromatin re-modelling proteins.
Length = 140
Score = 35.3 bits (82), Expect = 0.021
Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 412 SREAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEE 471
+REA+ + + +++ L+ + R +K EK E K ++E E+ ++ EE
Sbjct: 46 AREARRWQLRTQKIMKDTQLRAKRLMREMLLFWKKNEKEERELRKRAEKEALEQAKKEEE 105
Query: 472 -KEAKRQMKK 480
+EAKRQ +K
Sbjct: 106 LREAKRQQRK 115
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 37.0 bits (85), Expect = 0.023
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 3/86 (3%)
Query: 410 RLSREAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRW 469
+ + EAK KA++ + + + A K +A AA + E E E ++ + ++++
Sbjct: 1315 KKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKE 1374
Query: 470 EEKEAKRQMKKKTPKMK---QLKVKA 492
E K+ KKK + K + K KA
Sbjct: 1375 EAKKKADAAKKKAEEKKKADEAKKKA 1400
Score = 34.7 bits (79), Expect = 0.15
Identities = 24/89 (26%), Positives = 45/89 (50%), Gaps = 6/89 (6%)
Query: 410 RLSREAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEED---PEKQ 466
+ + EAK KA++++ + +E +A+ A + EEK++ ++ K EE E +
Sbjct: 1391 KKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAK 1450
Query: 467 RRWEEKEAKRQMKKKTP---KMKQLKVKA 492
++ EE + + KKK K + K KA
Sbjct: 1451 KKAEEAKKAEEAKKKAEEAKKADEAKKKA 1479
Score = 33.6 bits (76), Expect = 0.28
Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 412 SREAKSKADKNRHRVEEAFLKTTHVAR-AEAAALRKEEKRRLEKEKIMQEEDPEKQRRWE 470
+ A +A+ + E A K + A+AA + EEK++ ++ K EED +K +
Sbjct: 1352 AEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELK 1411
Query: 471 EKEAKRQMKKKTPKMKQLKVKA 492
+ A ++ + K + K KA
Sbjct: 1412 KAAAAKKKADEAKKKAEEKKKA 1433
Score = 33.2 bits (75), Expect = 0.38
Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 414 EAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEED---PEKQRRWE 470
EAK KA++ + + +EA K +A+ A + EE ++ E+ K EE E +++ E
Sbjct: 1422 EAKKKAEEKK-KADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAE 1480
Query: 471 EKEAKRQMKKKTPKMKQ 487
E + + KKK + K+
Sbjct: 1481 EAKKADEAKKKAEEAKK 1497
Score = 33.2 bits (75), Expect = 0.39
Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 410 RLSREAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRW 469
+ + EAK KA++ + + EEA K +A+ A + EE ++ ++ K EE +K
Sbjct: 1444 KKADEAKKKAEEAK-KAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKA--- 1499
Query: 470 EEKEAKRQMKKKTPKMKQ 487
+E + + KKK + K+
Sbjct: 1500 DEAKKAAEAKKKADEAKK 1517
Score = 32.4 bits (73), Expect = 0.69
Identities = 19/74 (25%), Positives = 37/74 (50%)
Query: 414 EAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEEKE 473
E KAD+ + + EEA K +A A + +E ++ E+ K E ++ + ++
Sbjct: 1480 EEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEA 1539
Query: 474 AKRQMKKKTPKMKQ 487
K + KKK ++K+
Sbjct: 1540 KKAEEKKKADELKK 1553
Score = 32.4 bits (73), Expect = 0.72
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 3/77 (3%)
Query: 414 EAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEE---DPEKQRRWE 470
E K KAD+ + + EE K + +A AA + +E ++ +EK +E E+ ++ +
Sbjct: 1388 EEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKAD 1447
Query: 471 EKEAKRQMKKKTPKMKQ 487
E + K + KK + K+
Sbjct: 1448 EAKKKAEEAKKAEEAKK 1464
Score = 32.0 bits (72), Expect = 0.88
Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 410 RLSREAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRW 469
+ + EAK KA++ + + +EA K +AE A + EE ++ ++ K E E ++
Sbjct: 1431 KKADEAKKKAEEAK-KADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAE---EAKKAD 1486
Query: 470 EEKEAKRQMKKKTPKMKQ 487
E K+ + KKK + K+
Sbjct: 1487 EAKKKAEEAKKKADEAKK 1504
Score = 31.6 bits (71), Expect = 1.1
Identities = 28/83 (33%), Positives = 43/83 (51%), Gaps = 8/83 (9%)
Query: 412 SREAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEK---EKIMQEEDPEK--- 465
+ EAK KAD + + EEA K A+AEA A E + EK + +EE +K
Sbjct: 1324 AEEAKKKADAAKKKAEEA-KKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADA 1382
Query: 466 -QRRWEEKEAKRQMKKKTPKMKQ 487
+++ EEK+ + KKK + K+
Sbjct: 1383 AKKKAEEKKKADEAKKKAEEDKK 1405
Score = 31.6 bits (71), Expect = 1.1
Identities = 18/87 (20%), Positives = 37/87 (42%), Gaps = 8/87 (9%)
Query: 414 EAKSKADKNRHRVE----EAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEK---- 465
E KAD+ + E + K +A+ A + EE ++ ++ K EE +K
Sbjct: 1275 EEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAA 1334
Query: 466 QRRWEEKEAKRQMKKKTPKMKQLKVKA 492
+++ EE + + K + + +A
Sbjct: 1335 KKKAEEAKKAAEAAKAEAEAAADEAEA 1361
Score = 31.6 bits (71), Expect = 1.2
Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 418 KADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEED---PEKQRRWEEKEA 474
KA + + +EA K +A+ A + EE ++ ++ K EE E +++ EE +
Sbjct: 1412 KAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKK 1471
Query: 475 KRQMKKKTP---KMKQLKVKA 492
+ KKK K + K KA
Sbjct: 1472 ADEAKKKAEEAKKADEAKKKA 1492
Score = 31.3 bits (70), Expect = 1.4
Identities = 20/82 (24%), Positives = 42/82 (51%)
Query: 410 RLSREAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRW 469
+ + EAK KA++ + + +EA +A+ A +E K+ E +K + + ++ ++
Sbjct: 1483 KKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKA 1542
Query: 470 EEKEAKRQMKKKTPKMKQLKVK 491
EEK+ ++KK K + K
Sbjct: 1543 EEKKKADELKKAEELKKAEEKK 1564
Score = 30.9 bits (69), Expect = 1.9
Identities = 21/92 (22%), Positives = 46/92 (50%), Gaps = 6/92 (6%)
Query: 404 DRVKRFRLSREAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDP 463
D+ R + EAK + R+EE + +A +K E+ +++ E++ + E+
Sbjct: 1575 DKNMALRKAEEAKKAEEA---RIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEE 1631
Query: 464 EK---QRRWEEKEAKRQMKKKTPKMKQLKVKA 492
+K Q + +E E K++ ++ ++ K+KA
Sbjct: 1632 KKKVEQLKKKEAEEKKKAEELKKAEEENKIKA 1663
Score = 30.9 bits (69), Expect = 2.3
Identities = 19/80 (23%), Positives = 39/80 (48%), Gaps = 6/80 (7%)
Query: 414 EAKSKADKNRHRVEEAFLKTTHVARAE------AAALRKEEKRRLEKEKIMQEEDPEKQR 467
E K KA++ + EE +K A+ A +K E+ + + +++E E ++
Sbjct: 1644 EEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKK 1703
Query: 468 RWEEKEAKRQMKKKTPKMKQ 487
E K+ + + KKK ++K+
Sbjct: 1704 AEELKKKEAEEKKKAEELKK 1723
Score = 30.5 bits (68), Expect = 2.7
Identities = 15/78 (19%), Positives = 39/78 (50%)
Query: 410 RLSREAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRW 469
++ E KA++ + +VE+ K + + EE+ +++ + ++ + +K++
Sbjct: 1619 KIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAE 1678
Query: 470 EEKEAKRQMKKKTPKMKQ 487
E K+A+ KK +K+
Sbjct: 1679 EAKKAEEDEKKAAEALKK 1696
Score = 30.1 bits (67), Expect = 3.7
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 412 SREAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEE 471
+ EAK KAD+ + + EA K +AE A E K+ E +K + + E++++ +E
Sbjct: 1492 AEEAKKKADEAK-KAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADE 1550
Query: 472 KEAKRQMKKKTPKMK 486
+ ++KK K K
Sbjct: 1551 LKKAEELKKAEEKKK 1565
Score = 29.7 bits (66), Expect = 5.2
Identities = 17/86 (19%), Positives = 42/86 (48%), Gaps = 2/86 (2%)
Query: 405 RVKRFRLSREAKSKADKNRHRVEEAFLKTTHVARAE-AAALRKEEKRRLEKEKIMQEEDP 463
+ + + + E K K ++ + + E K + +AE ++ E+ + +E + E+
Sbjct: 1621 KAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEA 1680
Query: 464 EKQRRWEEKEAKRQMKKKTPKMKQLK 489
+K +EK+A +KK+ + K+ +
Sbjct: 1681 KKAEE-DEKKAAEALKKEAEEAKKAE 1705
Score = 29.7 bits (66), Expect = 5.3
Identities = 20/94 (21%), Positives = 45/94 (47%), Gaps = 8/94 (8%)
Query: 405 RVKRFRLSREAKSKADKNRHRVEEAFLKTTHVARAEAAALRK-------EEKRRLEKEKI 457
+ + + + E + KA + + E K + + EA +K EE+ +++ E+
Sbjct: 1676 KAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEA 1735
Query: 458 MQEEDPEKQRRWEEKEAKRQMKKKTPKMKQLKVK 491
+E + +K ++ EE + + KKK +K+ + K
Sbjct: 1736 KKEAEEDK-KKAEEAKKDEEEKKKIAHLKKEEEK 1768
Score = 29.3 bits (65), Expect = 5.7
Identities = 22/74 (29%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 414 EAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEEKE 473
E KA++++ + EEA K + A AL+KE + + E++ ++E EK++ E K+
Sbjct: 1665 EEAKKAEEDKKKAEEA-KKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKK 1723
Query: 474 AKRQMKKKTPKMKQ 487
A+ + K K + K+
Sbjct: 1724 AEEENKIKAEEAKK 1737
Score = 29.3 bits (65), Expect = 6.4
Identities = 23/94 (24%), Positives = 45/94 (47%), Gaps = 6/94 (6%)
Query: 405 RVKRFRLSREAKSKADKNRHRVEEAFLKTTHVAR--AEAAALRKEEKRRLEKEKIMQE-E 461
+ + + E KA++ R+ E + +A AA++ EE R+ ++ K +E +
Sbjct: 1231 KAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKK 1290
Query: 462 DPEKQRRWEEKEAKRQMKKKTP---KMKQLKVKA 492
++ ++ EEK+ + KKK K + K KA
Sbjct: 1291 KADEAKKAEEKKKADEAKKKAEEAKKADEAKKKA 1324
>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell
envelope biogenesis, outer membrane].
Length = 387
Score = 36.5 bits (84), Expect = 0.026
Identities = 28/89 (31%), Positives = 39/89 (43%), Gaps = 5/89 (5%)
Query: 407 KRFRLSREAKSKADKNRHRVEEAFLKTTHVAR---AEAAALRKEEKRRLEKEKIMQEEDP 463
+ + + EAK KA++ EEA K A AEA A EK + E E + E
Sbjct: 161 AKLKAAAEAKKKAEEAAKAAEEAKAKAEAAAAKKKAEAEAKAAAEKAKAEAEAKAKAE-- 218
Query: 464 EKQRRWEEKEAKRQMKKKTPKMKQLKVKA 492
+K E++A + KK K K K A
Sbjct: 219 KKAEAAAEEKAAAEKKKAAAKAKADKAAA 247
Score = 31.1 bits (70), Expect = 1.2
Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 2/76 (2%)
Query: 407 KRFRLSREAKSKADKNRH-RVEEAFLKTTHVARAEAAALRKEEKRRL-EKEKIMQEEDPE 464
R + + + K ++ R + E+ + AE L++ EK RL +E+ Q E+ E
Sbjct: 65 GRIQSQQSSAKKGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAE 124
Query: 465 KQRRWEEKEAKRQMKK 480
KQ + E+K+ + Q +K
Sbjct: 125 KQAQLEQKQQEEQARK 140
>gnl|CDD|227490 COG5161, SFT1, Pre-mRNA cleavage and polyadenylation specificity
factor [RNA processing and modification].
Length = 1319
Score = 34.9 bits (80), Expect = 0.10
Identities = 23/121 (19%), Positives = 42/121 (34%), Gaps = 12/121 (9%)
Query: 272 LIRPSTDQLSMSFDLGKEDMDSFSLYCPERKSGDKFNLPSGFNVMSEIAEVSSSLIDSKF 331
+ + S S+ G + KF+ PS SE+ ++ID F
Sbjct: 164 MFQMSKRHFSIFPSQGTNTFNKRK----RTLFPGKFSAPSKVLKFSELDGKIKNIIDFVF 219
Query: 332 LTIVNKFSDLIDYIHISDQFSGPKQTEETTLTKLPDVKKVILFNFNLQMGQLSIQDTIDE 391
L + + + Y PK + T L + I+F +L G+ ++ D
Sbjct: 220 LENYSIPTVALLY--------DPKLSLPRKYTILKNPYNAIVFTLDLGAGRSAVIDEFLV 271
Query: 392 M 392
+
Sbjct: 272 L 272
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 34.2 bits (79), Expect = 0.18
Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 17/72 (23%)
Query: 413 REAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKR-RLEKEKIMQEEDPEKQRRWEE 471
R+AK++ R +E +AE A R E ++ RLE+EK ++ R ++
Sbjct: 432 RQAKAEI---RAIEQEK-------KKAEEAKARFEARQARLEREKA------AREARHKK 475
Query: 472 KEAKRQMKKKTP 483
R K K
Sbjct: 476 AAEARAAKDKDA 487
>gnl|CDD|206108 pfam13937, DUF4212, Domain of unknown function (DUF4212). This
family includes several putative integral membrane
proteins.
Length = 81
Score = 31.0 bits (71), Expect = 0.22
Identities = 11/38 (28%), Positives = 19/38 (50%)
Query: 17 MKFKLKLSILLLLVTFLVSYGVHGQFNDQFKDDEFADF 54
+ L+L +LL++ F+VS+GV F + F
Sbjct: 7 WRENLRLIAILLVIWFVVSFGVGILFAPELNTITIGGF 44
>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein. TolA couples the inner
membrane complex of itself with TolQ and TolR to the
outer membrane complex of TolB and OprL (also called
Pal). Most of the length of the protein consists of
low-complexity sequence that may differ in both length
and composition from one species to another,
complicating efforts to discriminate TolA (the most
divergent gene in the tol-pal system) from paralogs such
as TonB. Selection of members of the seed alignment and
criteria for setting scoring cutoffs are based largely
conserved operon struction. //The Tol-Pal complex is
required for maintaining outer membrane integrity. Also
involved in transport (uptake) of colicins and
filamentous DNA, and implicated in pathogenesis.
Transport is energized by the proton motive force. TolA
is an inner membrane protein that interacts with
periplasmic TolB and with outer membrane porins ompC,
phoE and lamB [Transport and binding proteins, Other,
Cellular processes, Pathogenesis].
Length = 346
Score = 33.7 bits (77), Expect = 0.23
Identities = 16/80 (20%), Positives = 37/80 (46%), Gaps = 1/80 (1%)
Query: 413 REAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEEK 472
+ +A+K R E+A K A A ++ E+ + E+ ++ + K ++ E
Sbjct: 74 EQQAEEAEKQR-AAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEA 132
Query: 473 EAKRQMKKKTPKMKQLKVKA 492
+AK + + + ++ K +A
Sbjct: 133 KAKAEAEAEKKAKEEAKKQA 152
Score = 32.9 bits (75), Expect = 0.34
Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 4/79 (5%)
Query: 414 EAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEEKE 473
EAK+KA+ + + K A EA A E ++ E + E K + E +
Sbjct: 131 EAKAKAEAEAEKKAKEEAK--KQAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAK--AEAK 186
Query: 474 AKRQMKKKTPKMKQLKVKA 492
AK + ++ K + K KA
Sbjct: 187 AKAKAEEAKAKAEAAKAKA 205
Score = 31.3 bits (71), Expect = 0.95
Identities = 21/69 (30%), Positives = 28/69 (40%), Gaps = 4/69 (5%)
Query: 413 REAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEEK 472
E K+K + + EEA K A AEA E K++ E E + E K + E K
Sbjct: 140 AEKKAKEEAKKQAEEEAKAK----AAAEAKKKAAEAKKKAEAEAKAKAEAKAKAKAEEAK 195
Query: 473 EAKRQMKKK 481
K K
Sbjct: 196 AKAEAAKAK 204
Score = 31.0 bits (70), Expect = 1.3
Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 3/80 (3%)
Query: 414 EAKSKADKNRHRVEEAFLKTTHVAR-AEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEEK 472
E + A++ R + E A+ AE AA + EEK++ +E ++ K + E
Sbjct: 81 EKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAK--AEA 138
Query: 473 EAKRQMKKKTPKMKQLKVKA 492
EA+++ K++ K + + KA
Sbjct: 139 EAEKKAKEEAKKQAEEEAKA 158
Score = 28.6 bits (64), Expect = 8.1
Identities = 16/79 (20%), Positives = 35/79 (44%), Gaps = 6/79 (7%)
Query: 414 EAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEEKE 473
+A +A++ + + EEA A+ A A K E +K K ++ E++ + +
Sbjct: 109 QAAKQAEEKQKQAEEA------KAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAA 162
Query: 474 AKRQMKKKTPKMKQLKVKA 492
++ + K + + KA
Sbjct: 163 EAKKKAAEAKKKAEAEAKA 181
>gnl|CDD|219978 pfam08701, GN3L_Grn1, GNL3L/Grn1 putative GTPase. Grn1 (yeast) and
GNL3L (human) are putative GTPases which are required
for growth and play a role in processing of nucleolar
pre-rRNA. This family contains a potential nuclear
localisation signal.
Length = 80
Score = 30.3 bits (69), Expect = 0.38
Identities = 10/28 (35%), Positives = 22/28 (78%)
Query: 454 KEKIMQEEDPEKQRRWEEKEAKRQMKKK 481
KE+I++E + +K+++ EEKE +++ +K
Sbjct: 44 KEEILEEIEEKKRKQEEEKERRKEARKA 71
>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional.
Length = 1021
Score = 33.2 bits (75), Expect = 0.40
Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 9/81 (11%)
Query: 391 EMKPLMQFVFYTLDRVKRFRLSREAKSKADKNR---HRVEEAFLKTTHVARAEAAALRKE 447
EMK L + L+R +R RL RE + ++ R R+E L+ + R L +E
Sbjct: 451 EMKILEKKRIERLEREERERLERERMERIERERLERERLERERLERDRLERDRLDRLERE 510
Query: 448 EKRRLEKEKIMQEEDPEKQRR 468
RLE++++ EK RR
Sbjct: 511 RVDRLERDRL------EKARR 525
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 31.8 bits (73), Expect = 0.78
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 6/83 (7%)
Query: 402 TLDRVKRFRLSREA----KSKADKNRHRVEEAFLKTTHVARAEAAALRKEE--KRRLEKE 455
T + ++ S++A K +K + EE + A A +EE K + E+E
Sbjct: 395 TEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEE 454
Query: 456 KIMQEEDPEKQRRWEEKEAKRQM 478
K +EE+ E+++ EE++ K+Q
Sbjct: 455 KEEEEEEAEEEKEEEEEKKKKQA 477
>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein
TolA; Provisional.
Length = 387
Score = 31.7 bits (72), Expect = 0.89
Identities = 14/79 (17%), Positives = 27/79 (34%)
Query: 414 EAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEEKE 473
K+ A+ + EA K A+ +A A K++ K+K E + E +
Sbjct: 176 AKKAAAEAKKKAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKKAAAEAKAAAAKAAAEAK 235
Query: 474 AKRQMKKKTPKMKQLKVKA 492
A + ++
Sbjct: 236 AAAEKAAAAKAAEKAAAAK 254
Score = 29.8 bits (67), Expect = 3.4
Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 5/87 (5%)
Query: 410 RLSREAKSKADKNRHRVEEAFLKTTHVARAEAAA---LRKEEKRRL-EKEKIMQEEDPEK 465
R ++ KS R ++ + + + +AA L++ EK RL +E+ Q E+ K
Sbjct: 66 RQQQQQKSAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAK 125
Query: 466 QRRWEEKEAKRQMKKKTPKMKQLKVKA 492
Q ++K+A+ K K K +A
Sbjct: 126 QAALKQKQAEEAAAKAAAAAK-AKAEA 151
Score = 29.4 bits (66), Expect = 5.3
Identities = 22/80 (27%), Positives = 33/80 (41%), Gaps = 5/80 (6%)
Query: 414 EAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWE-EK 472
EA +A + + EEA K A+A+A A E +R + +K+ E K
Sbjct: 122 EAAKQAALKQKQAEEAAAKAAAAAKAKAEA----EAKRAAAAAKKAAAEAKKKAEAEAAK 177
Query: 473 EAKRQMKKKTPKMKQLKVKA 492
+A + KKK K A
Sbjct: 178 KAAAEAKKKAEAEAAAKAAA 197
>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain.
Transcription of the anti-viral guanylate-binding
protein (GBP) is induced by interferon-gamma during
macrophage induction. This family contains GBP1 and
GPB2, both GTPases capable of binding GTP, GDP and GMP.
Length = 297
Score = 31.5 bits (72), Expect = 0.90
Identities = 13/50 (26%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 432 KTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEEKEAKRQMKKK 481
K RA+A A E++ EK+K ++ ++R ++E +Q+ +K
Sbjct: 204 KAIEAERAKAEAAEAEQELLREKQKEEEQMMEAQERSYQEH--VKQLIEK 251
>gnl|CDD|221028 pfam11208, DUF2992, Protein of unknown function (DUF2992). This
bacterial family of proteins has no known function.
However, the cis-regulatory yjdF motif, just upstream
from the gene encoding the proteins for this family, is
a small non-coding RNA, Rfam:RF01764. The yjdF motif is
found in many Firmicutes, including Bacillus subtilis.
In most cases, it resides in potential 5' UTRs of
homologues of the yjdF gene whose function is unknown.
However, in Streptococcus thermophilus, a yjdF RNA motif
is associated with an operon whose protein products
synthesise nicotinamide adenine dinucleotide (NAD+).
Also, the S. thermophilus yjdF RNA lacks typical yjdF
motif consensus features downstream of and including the
P4 stem. Thus, if yjdF RNAs are riboswitch aptamers, the
S. thermophilus RNAs might sense a distinct compound
that structurally resembles the ligand bound by other
yjdF RNAs. On the ohter hand, perhaps these RNAs have an
alternative solution forming a similar binding site, as
is observed with some SAM riboswitches.
Length = 132
Score = 30.3 bits (69), Expect = 1.0
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 5/46 (10%)
Query: 442 AALRKEEKRRLEKEKIMQEEDPEKQRRWEEKEAKRQMKKKTPKMKQ 487
AL+ E +R +++K K+++ EEKE KRQ+K++ K K
Sbjct: 89 QALKLEHERNKQEKKKRS-----KEKKEEEKERKRQLKQQKKKAKH 129
>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family. The organisation of
microtubules varies with the cell type and is presumably
controlled by tissue-specific microtubule-associated
proteins (MAPs). The 115-kDa epithelial MAP
(E-MAP-115/MAP7) has been identified as a
microtubule-stabilising protein predominantly expressed
in cell lines of epithelial origin. The binding of this
microtubule associated protein is nucleotide
independent.
Length = 171
Score = 30.8 bits (69), Expect = 1.1
Identities = 20/83 (24%), Positives = 46/83 (55%), Gaps = 1/83 (1%)
Query: 405 RVKRFRLSREAKSKADKNRHRVEEAFLKTTHV-ARAEAAALRKEEKRRLEKEKIMQEEDP 463
R +R + +E + + +++R EE + R E A R+EE+R EKE+ + +
Sbjct: 36 REQREQEEQERREQEEQDRLEREELKRRAAEERLRREEEARRQEEERAREKEEKAKRKAE 95
Query: 464 EKQRRWEEKEAKRQMKKKTPKMK 486
E++++ +E++ + Q +K+ + +
Sbjct: 96 EEEKQEQEEQERIQKQKEEAEAR 118
>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 = 31.2 bits (70), Expect = 1.5
Identities = 27/65 (41%), Positives = 36/65 (55%), Gaps = 14/65 (21%)
Query: 415 AKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEEKEA 474
A SK K R EEA K A+ EA +EE+ R EKEK E++ E++R E+EA
Sbjct: 573 ASSKLAKKR---EEAVEK----AKREAEQKAREERER-EKEK---EKERERER---EREA 618
Query: 475 KRQMK 479
+R K
Sbjct: 619 ERAAK 623
>gnl|CDD|215180 PLN02316, PLN02316, synthase/transferase.
Length = 1036
Score = 30.6 bits (69), Expect = 2.1
Identities = 31/108 (28%), Positives = 49/108 (45%), Gaps = 20/108 (18%)
Query: 396 MQFVFYTLDRV------KRFRLSREAKSKADKNRHR---VEEAFLKTTHVARAEAAALR- 445
M FVF+ V K F + E + D++ +EE + +A+ EA R
Sbjct: 214 MDFVFFNGQNVYDNNDHKDFCV--EIEGGMDEHSFEDFLLEEKRRELEKLAKEEAERERQ 271
Query: 446 KEEKRRLEKEKIMQEEDPEKQRRWEEKEAKRQMKKKTPKMKQLKVKAL 493
EE+RR E+EK E D +AK +++K+ K++ L KA
Sbjct: 272 AEEQRRREEEKAAMEAD--------RAQAKAEVEKRREKLQNLLKKAS 311
>gnl|CDD|233042 TIGR00598, rad14, DNA repair protein. All proteins in this family
for which functions are known are used for the
recognition of DNA damage as part of nucleotide excision
repair. This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 172
Score = 29.7 bits (67), Expect = 2.2
Identities = 18/44 (40%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 448 EKRRLEKEKIMQEEDPEKQRRWEEKEAKRQMKKKTPKMKQLKVK 491
EKR LE + D EK+RR E KE ++ KK K+K+L+
Sbjct: 83 EKRALEVWGSEEALDEEKERREESKEEMKE-KKFEKKLKELRRA 125
>gnl|CDD|173965 cd08045, TAF4, TATA Binding Protein (TBP) Associated Factor 4
(TAF4) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 4 (TAF4) is one of several TAFs that bind TBP and
are involved in forming the Transcription Factor IID
(TFIID) complex. TFIID is one of seven General
Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE,
TFIIF, and TFIID) that are involved in accurate
initiation of transcription by RNA polymerase II in
eukaryote. TFIID plays an important role in the
recognition of promoter DNA and assembly of the
pre-initiation complex. TFIID complex is composed of the
TBP and at least 13 TAFs. TAFs from various species were
originally named by their predicted molecular weight or
their electrophoretic mobility in polyacrylamide gels. A
new, unified nomenclature for the pol II TAFs has been
suggested to show the relationship between TAF orthologs
and paralogs. Several hypotheses are proposed for TAFs
functions such as serving as activator-binding sites,
core-promoter recognition or a role in essential
catalytic activity. Each TAF, with the help of a
specific activator, is required only for the expression
of subset of genes and is not universally involved for
transcription as are GTFs. In yeast and human cells,
TAFs have been found as components of other complexes
besides TFIID. Several TAFs interact via histone-fold
(HFD) motifs; HFD is the interaction motif involved in
heterodimerization of the core histones and their
assembly into nucleosome octamers. The minimal HFD
contains three alpha-helices linked by two loops and is
found in core histones, TAFS and many other
transcription factors. TFIID has a histone octamer-like
substructure. TAF4 domain interacts with TAF12 and makes
a novel histone-like heterodimer that binds DNA and has
a core promoter function of a subset of genes.
Length = 212
Score = 30.0 bits (68), Expect = 2.5
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 6/55 (10%)
Query: 414 EAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRR 468
E + ++ + EE AA R E+ R +K K MQ+E+ E+ R
Sbjct: 120 EQLEREEEEKRDEEERER------LLRAAKSRSEQSRLKQKAKEMQKEEDEEMRH 168
>gnl|CDD|234707 PRK00270, rpsU, 30S ribosomal protein S21; Reviewed.
Length = 64
Score = 27.5 bits (62), Expect = 2.5
Identities = 15/51 (29%), Positives = 31/51 (60%), Gaps = 8/51 (15%)
Query: 443 ALRKEEKRRLEKEKIMQE-------EDPEKQRRWEEKEAKRQMKKKTPKMK 486
ALR+ KR++EK I++E E P ++R+ ++ A+++ +KK + +
Sbjct: 15 ALRRF-KRKVEKAGILRELRRREFYEKPSEKRKRKKAAARKRRRKKLAREE 64
>gnl|CDD|223898 COG0828, RpsU, Ribosomal protein S21 [Translation, ribosomal
structure and biogenesis].
Length = 67
Score = 27.7 bits (62), Expect = 2.6
Identities = 17/53 (32%), Positives = 32/53 (60%), Gaps = 8/53 (15%)
Query: 443 ALRKEEKRRLEKEKIMQE-------EDPEKQRRWEEKEAKRQMKKKTPKMKQL 488
ALR+ KR++EKE I++E E P ++R+ ++ A+++ K+ K +Q
Sbjct: 15 ALRRF-KRKVEKEGILREMKEREFYEKPSEKRKRKKAAARKRKFKRLRKEQQR 66
>gnl|CDD|233222 TIGR00986, 3a0801s05tom22, mitochondrial import receptor subunit
Tom22. The mitochondrial protein translocase (MPT)
family, which brings nuclearly encoded preproteins into
mitochondria, is very complex with 19 currently
identified protein constituents.These proteins include
several chaperone proteins, four proteins of the outer
membrane translocase (Tom) import receptor, five
proteins of the Tom channel complex, five proteins of
the inner membrane translocase (Tim) and three "motor"
proteins. This family is specific for the Tom22 proteins
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 145
Score = 29.2 bits (65), Expect = 2.7
Identities = 15/38 (39%), Positives = 19/38 (50%)
Query: 71 VQQNVQETWEEEPVEAITEEDVMIEDEEDSDFEHFKDE 108
QQ Q+T E + DV ED DSDFE ++E
Sbjct: 12 FQQPEQQTVVEPEEDDEDFTDVDSEDSVDSDFESLEEE 49
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 30.2 bits (69), Expect = 2.8
Identities = 14/89 (15%), Positives = 35/89 (39%), Gaps = 2/89 (2%)
Query: 403 LDRVKRFRLSREAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEED 462
L ++ + E K + + + A+ +KE +++ + +Q+
Sbjct: 543 LKEAEKLKEELEEKKEKLQEEEDKLLEEAEKE--AQQAIKEAKKEADEIIKELRQLQKGG 600
Query: 463 PEKQRRWEEKEAKRQMKKKTPKMKQLKVK 491
+ E EA++++ K K ++ K K
Sbjct: 601 YASVKAHELIEARKRLNKANEKKEKKKKK 629
>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase
component YidC; Validated.
Length = 429
Score = 30.2 bits (68), Expect = 3.1
Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 3/61 (4%)
Query: 423 RHRVEEAFLKTTHVARAEAAALRKEE---KRRLEKEKIMQEEDPEKQRRWEEKEAKRQMK 479
E A +K T A A RK+E KRR + +I +E E+ A+R
Sbjct: 324 ELHAENAEIKKTRTAEKNEAKARKKEIAQKRRAAEREINREARQERAAAMARARARRAAV 383
Query: 480 K 480
K
Sbjct: 384 K 384
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 30.1 bits (69), Expect = 3.3
Identities = 19/81 (23%), Positives = 44/81 (54%), Gaps = 1/81 (1%)
Query: 414 EAKSKADKNRHRVE-EAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEEK 472
EAK + K R+ E E + + + E L+KEE + E + + E+ +++ E +
Sbjct: 61 EAKEEIHKLRNEFEKELRERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELE 120
Query: 473 EAKRQMKKKTPKMKQLKVKAL 493
+ +++++KK ++++L + L
Sbjct: 121 QKQQELEKKEEELEELIEEQL 141
>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein. The YqfQ-like protein family
includes the B. subtilis YqfQ protein, also known as
VrrA, which is functionally uncharacterized. This family
of proteins is found in bacteria. Proteins in this
family are typically between 146 and 237 amino acids in
length. There are two conserved sequence motifs: QYGP
and PKLY.
Length = 155
Score = 29.0 bits (65), Expect = 3.9
Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 8/77 (10%)
Query: 409 FRLSREAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRR 468
+++ RE S D+ EE+ T + + + E K + ++E + + EK
Sbjct: 85 WKIFRELSSSDDEEEETEEES---TDETEQEDPPETKTESKEKKKREVPKPKTEKEK--- 138
Query: 469 WEEKEAKRQMKKKTPKM 485
K ++ K PK+
Sbjct: 139 --PKTEPKKPKPSKPKL 153
>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit
RPA34.5. This is a family of proteins conserved from
yeasts to human. Subunit A34.5 of RNA polymerase I is a
non-essential subunit which is thought to help Pol I
overcome topological constraints imposed on ribosomal
DNA during the process of transcription.
Length = 193
Score = 28.9 bits (65), Expect = 4.7
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 427 EEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEEKEAKRQMKKKTPKMK 486
E K T + A + +EEK+ +K+K E EK+ + ++K+ K K + K K
Sbjct: 132 SETSEKETTAKVEKEAEVEEEEKKEKKKKK---EVKKEKKEK-KDKKEKMVEPKGSKKKK 187
Query: 487 QLKVK 491
+ K K
Sbjct: 188 KKKKK 192
>gnl|CDD|153367 cd07683, F-BAR_srGAP1, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase
Activating Protein 1. F-BAR domains are dimerization
modules that bind and bend membranes and are found in
proteins involved in membrane dynamics and actin
reorganization. Slit-Robo GTPase Activating Proteins
(srGAPs) are Rho GAPs that interact with Robo1, the
transmembrane receptor of Slit proteins. Slit proteins
are secreted proteins that control axon guidance and the
migration of neurons and leukocytes. Vertebrates contain
three isoforms of srGAPs. srGAP1, also called Rho
GTPase-Activating Protein 13 (ARHGAP13), is a Cdc42- and
RhoA-specific GAP and is expressed later in the
development of CNS (central nervous system) tissues. It
is an important downstream signaling molecule of Robo1.
srGAP1 contains an N-terminal F-BAR domain, a Rho GAP
domain, and a C-terminal SH3 domain. F-BAR domains form
banana-shaped dimers with a positively-charged concave
surface that binds to negatively-charged lipid
membranes. They can induce membrane deformation in the
form of long tubules.
Length = 253
Score = 28.9 bits (64), Expect = 5.0
Identities = 25/98 (25%), Positives = 50/98 (51%), Gaps = 5/98 (5%)
Query: 395 LMQFVFYTLDRVKRFRLSREAKSKADKNRHRVEEAF---LKTTHVARAE--AAALRKEEK 449
+M+F+ + D + F+ S+E + ++ +V +KT H+ E +A + +E
Sbjct: 101 IMRFMQISEDSTRMFKKSKEIAFQLHEDLMKVLNELYTVMKTYHMYHTESISAESKLKEA 160
Query: 450 RRLEKEKIMQEEDPEKQRRWEEKEAKRQMKKKTPKMKQ 487
+ E+++I + DP R E++ +R KK KMK+
Sbjct: 161 EKQEEKQIGRSGDPVFHIRLEDRHQRRSSVKKIEKMKE 198
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 29.1 bits (66), Expect = 5.1
Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 4/61 (6%)
Query: 53 DFEEFEDPEEALLKESLNVQQNVQETWEEEPVEAITEEDVMIEDEEDSDFEHFKDEEEFE 112
D F + E + V+ W++ E + E + +D+ D D+ DE++ E
Sbjct: 327 DLMTFIEENPREEAEEAEAPEKVEFMWDDYHREQLEEVEEEDDDDWDDDW----DEDDDE 382
Query: 113 G 113
G
Sbjct: 383 G 383
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit
Rpc31. RNA polymerase III contains seventeen subunits
in yeasts and in human cells. Twelve of these are akin
to RNA polymerase I or II and the other five are RNA pol
III-specific, and form the functionally distinct groups
(i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31,
Rpc34 and Rpc82 form a cluster of enzyme-specific
subunits that contribute to transcription initiation in
S.cerevisiae and H.sapiens. There is evidence that these
subunits are anchored at or near the N-terminal Zn-fold
of Rpc1, itself prolonged by a highly conserved but RNA
polymerase III-specific domain.
Length = 221
Score = 29.0 bits (65), Expect = 5.6
Identities = 18/71 (25%), Positives = 30/71 (42%)
Query: 43 NDQFKDDEFADFEEFEDPEEALLKESLNVQQNVQETWEEEPVEAITEEDVMIEDEEDSDF 102
+E D +E E LKE + ++ +EE E EED +D++D D
Sbjct: 138 KVGLFTEEEEDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDFDDDDDDDD 197
Query: 103 EHFKDEEEFEG 113
+ + E F+
Sbjct: 198 DDYNAENYFDN 208
>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27. This protein forms
the C subunit of DNA polymerase delta. It carries the
essential residues for binding to the Pol1 subunit of
polymerase alpha, from residues 293-332, which are
characterized by the motif D--G--VT, referred to as the
DPIM motif. The first 160 residues of the protein form
the minimal domain for binding to the B subunit, Cdc1,
of polymerase delta, the final 10 C-terminal residues,
362-372, being the DNA sliding clamp, PCNA, binding
motif.
Length = 427
Score = 29.0 bits (65), Expect = 5.7
Identities = 16/85 (18%), Positives = 38/85 (44%), Gaps = 8/85 (9%)
Query: 412 SREAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRR--- 468
+ D++ E+ + + +E KE+++R +K+M++ED +++
Sbjct: 258 ESAEPTGLDEDED--EDEPKPSGERSDSEEETEEKEKEKRKRLKKMMEDEDEDEEMEIVP 315
Query: 469 ---WEEKEAKRQMKKKTPKMKQLKV 490
EE+E++ PK ++ K
Sbjct: 316 ESPVEEEESEEPEPPPLPKKEEEKE 340
>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 926
Score = 29.1 bits (65), Expect = 6.1
Identities = 23/104 (22%), Positives = 42/104 (40%), Gaps = 3/104 (2%)
Query: 389 IDEMKPLMQFVFYTLDRVKRFRLSREAKSKADKNRHRVEEAFLKTTHVARAEAAALRKE- 447
I + + +F F + F R + + K+ +V A L TT +A A A +K
Sbjct: 745 IRGSQAIPKFCFNEDLEEEEFEYPRMYEEASGKSVRKVNTAVLSTT--IKAAARAKQKPK 802
Query: 448 EKRRLEKEKIMQEEDPEKQRRWEEKEAKRQMKKKTPKMKQLKVK 491
EK +KE ++ E + + + + P + +K K
Sbjct: 803 EKGPNDKEIKIESPSVETEGERCTIKQREEKGIDAPAILNVKKK 846
>gnl|CDD|235322 PRK04950, PRK04950, ProP expression regulator; Provisional.
Length = 213
Score = 28.4 bits (64), Expect = 6.7
Identities = 15/68 (22%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 426 VEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEEKEAKRQMKKKTPKM 485
VE A K A+A+ A R E++ + + +E+ P ++R+ + K +++ K + K
Sbjct: 96 VEHA-RKQLEEAKAKVQAQRAEQQAKKREAAGEKEKAPRRERKPKPKAPRKKRKPRAQKP 154
Query: 486 KQLKVKAL 493
+
Sbjct: 155 EPQHTPVS 162
>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein. This
family includes the radial spoke head proteins RSP4 and
RSP6 from Chlamydomonas reinhardtii, and several
eukaryotic homologues, including mammalian RSHL1, the
protein product of a familial ciliary dyskinesia
candidate gene.
Length = 481
Score = 28.9 bits (65), Expect = 7.1
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 11/74 (14%)
Query: 47 KDDEFADFEEFEDPEEALLKESLN----VQQNV----QETWEEEPVEAITEEDVMIEDEE 98
+ DE + +FE E L +SL+ Q++ + TW + EE EDEE
Sbjct: 301 ERDELEENPDFEGLEVRELADSLDNWVHHVQHILPQGRCTWVNPEQKDEEEEQ---EDEE 357
Query: 99 DSDFEHFKDEEEFE 112
+ + E +E E E
Sbjct: 358 EEEEEEEPEEPEPE 371
>gnl|CDD|221389 pfam12037, DUF3523, Domain of unknown function (DUF3523). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 257 to 277 amino acids in length. This domain is
found associated with pfam00004. This domain has a
conserved LER sequence motif.
Length = 276
Score = 28.6 bits (64), Expect = 7.2
Identities = 17/86 (19%), Positives = 38/86 (44%), Gaps = 9/86 (10%)
Query: 415 AKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEE--- 471
+++A R RVE + T + + R + + L +++ Q+E +++R+ EE
Sbjct: 78 QQAQAKLERARVEAEERRKTLQEQTQQEQQRAQYQDELARKR-YQKELEQQRRQNEELLK 136
Query: 472 ---KEAKRQ--MKKKTPKMKQLKVKA 492
+ RQ M++ T + +
Sbjct: 137 MQEESVLRQEAMRRATEEEILEMRRE 162
>gnl|CDD|150884 pfam10278, Med19, Mediator of RNA pol II transcription subunit 19.
Med19 represents a family of conserved proteins which
are members of the multi-protein co-activator Mediator
complex. Mediator is required for activation of RNA
polymerase II transcription by DNA binding
transactivators.
Length = 178
Score = 28.3 bits (63), Expect = 7.4
Identities = 17/69 (24%), Positives = 39/69 (56%), Gaps = 8/69 (11%)
Query: 416 KSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEEKEAK 475
K K +HR ++ + T +++ L+ EK+ +K+ E+D E++++ +KE K
Sbjct: 112 KHKHKHKKHRTQDPLPEETP---SDSEGLKGHEKKHKKKKH---EDDKERKKK--KKEKK 163
Query: 476 RQMKKKTPK 484
++ K+ +P+
Sbjct: 164 KKKKRHSPE 172
>gnl|CDD|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO. Bacillus
spores are protected by a protein shell consisting of
over 50 different polypeptides, known as the coat. This
family of proteins has an important morphogenetic role
in coat assembly, it is involved in the assembly of at
least 5 different coat proteins including CotB, CotG,
CotS, CotSA and CotW. It is likely to act at a late
stage of coat assembly.
Length = 185
Score = 28.3 bits (63), Expect = 7.7
Identities = 22/106 (20%), Positives = 42/106 (39%), Gaps = 7/106 (6%)
Query: 385 IQDTIDEMKPLMQFVFYTLDRVKRFRLSREAKSKADKNRHRVEEAFLKTTHVARAEAAAL 444
+Q ++E K MQ F + + +E + + + H + + AE
Sbjct: 16 VQPKLEEAKANMQKTF-----IIKKADEKEEEKEN-SDEHVKSKEEEQKIEYEEAEKEKE 69
Query: 445 RKEEKRRLEKEKIMQEEDPEKQRRWEEKEA-KRQMKKKTPKMKQLK 489
E +R E+ +EE +++ + EE E K+Q + K K
Sbjct: 70 AGEPEREDIAEQQEKEEIAQEEEKEEEAEDVKQQEVFSFKRKKPFK 115
>gnl|CDD|240439 PTZ00491, PTZ00491, major vault protein; Provisional.
Length = 850
Score = 28.8 bits (65), Expect = 8.7
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 437 ARAEAAALRKEEKRRLEKEKIMQEEDPEKQRR-WEEKEAK 475
AR +A L +E + RLE++K+ + E+QR E +A+
Sbjct: 668 ARHQAELLEQEARGRLERQKMHDKAKAEEQRTKLLELQAE 707
>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168). This
family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 142
Score = 27.7 bits (62), Expect = 8.8
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 438 RAEAAALRKEEK--RRLEKEKIMQEEDPEKQRRWEEKEAK----RQMKKKTPKMKQLKVK 491
R E L ++ ++ +++ Q++ EK+R+ EEK AK RQ KK+ K K+ K
Sbjct: 46 RREYERLELMDEKWKKETEDEEFQQKREEKKRKDEEKTAKKRAKRQKKKQKKKKKKKAKK 105
Query: 492 A 492
Sbjct: 106 G 106
>gnl|CDD|225664 COG3122, COG3122, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 215
Score = 28.0 bits (62), Expect = 8.8
Identities = 9/46 (19%), Positives = 20/46 (43%)
Query: 437 ARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEEKEAKRQMKKKT 482
A A + + +LE++K + E+ + E K +Q+ +
Sbjct: 75 REAYRIAAEENKAEQLERDKQLSEQQKQAALAKEYKAQVKQLIEMN 120
>gnl|CDD|221371 pfam12004, DUF3498, Domain of unknown function (DUF3498). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 433 to 538 amino acids in length. This domain is
found associated with pfam00616, pfam00168. This domain
has two conserved sequence motifs: DLQ and PLSFQNP.
Length = 489
Score = 28.5 bits (63), Expect = 8.9
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 2/75 (2%)
Query: 414 EAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEEKE 473
E + + E+ + R L + E+R L +E+ MQ+ E Q R E+ E
Sbjct: 356 EENREEGTQAEKYEQEIARLKERLRVSVRRLEEYERRLLGQEQQMQKLLQEYQARLEDSE 415
Query: 474 A--KRQMKKKTPKMK 486
+RQ ++K +MK
Sbjct: 416 ERLRRQQEEKDSQMK 430
>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 = 28.7 bits (64), Expect = 9.1
Identities = 17/80 (21%), Positives = 34/80 (42%)
Query: 412 SREAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEEDPEKQRRWEE 471
+ + K +K + + + + EA R +++ EKEK ++E ++ + E
Sbjct: 108 KEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRE 167
Query: 472 KEAKRQMKKKTPKMKQLKVK 491
+ + KK PK K K
Sbjct: 168 RVRAKSRPKKPPKKKPPNKK 187
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 28.4 bits (64), Expect = 9.5
Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 10/83 (12%)
Query: 414 EAKSKADKNRHRVEEAFLKTTHVARAEAAALRKEEKRRLEKEKIMQEED---PEKQRRWE 470
EAK + K R +E + L++ E+R L++E+ + + +K+ E
Sbjct: 55 EAKEEVHKLRAELEREL-------KERRNELQRLERRLLQREETLDRKMESLDKKEENLE 107
Query: 471 EKEAKRQMKKKTPKMKQLKVKAL 493
+KE + K+K K+ +++ L
Sbjct: 108 KKEKELSNKEKNLDEKEEELEEL 130
>gnl|CDD|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit
[Transcription].
Length = 175
Score = 27.8 bits (62), Expect = 9.6
Identities = 18/57 (31%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 47 KDDEFADFEEFEDPEEALLKESLNVQQNVQETWEEEPVEAITEEDVMIEDEEDSDFE 103
+DE E+ E+ EE +SL+ + + ++ ++E VE + E+D + EDE+D + E
Sbjct: 114 DEDELDYDEDKEE-EEDDEVDSLDDENDDEDEDDDEIVEILIEDDEVDEDEDDDEDE 169
>gnl|CDD|226078 COG3548, COG3548, Predicted integral membrane protein [Function
unknown].
Length = 197
Score = 28.1 bits (63), Expect = 9.7
Identities = 10/53 (18%), Positives = 22/53 (41%), Gaps = 7/53 (13%)
Query: 130 ITIQDIPMHLRSNWDSYYLELLMIAGLVAYIINFITGRNKNFKLATHWINTHR 182
+TI + + + +++ L+ Y ++F+ +A W N HR
Sbjct: 27 MTIMVLEIKVPKGGGRLQALAELLSSLIIYALSFLV-------VAIFWFNHHR 72
>gnl|CDD|191187 pfam05087, Rota_VP2, Rotavirus VP2 protein. Rotavirus particles
consist of three concentric proteinaceous capsid layers.
The innermost capsid (core) is made of VP2. The genomic
RNA and the two minor proteins VP1 and VP3 are
encapsidated within this layer. The N-terminus of
rotavirus VP2 is necessary for the encapsidation of VP1
and VP3.
Length = 887
Score = 28.4 bits (63), Expect = 10.0
Identities = 12/39 (30%), Positives = 18/39 (46%)
Query: 443 ALRKEEKRRLEKEKIMQEEDPEKQRRWEEKEAKRQMKKK 481
A R + + MQE+D EKQ + E K ++ K
Sbjct: 2 AYRNRREANINNNDRMQEKDDEKQDQKNRMELKEKVLDK 40
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 0.132 0.374
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,298,360
Number of extensions: 2542917
Number of successful extensions: 5059
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4553
Number of HSP's successfully gapped: 327
Length of query: 493
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 392
Effective length of database: 6,457,848
Effective search space: 2531476416
Effective search space used: 2531476416
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: 61 (27.2 bits)