RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14582
(1689 letters)
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 444 bits (1145), Expect = e-137
Identities = 208/662 (31%), Positives = 294/662 (44%), Gaps = 68/662 (10%)
Query: 815 DEIHLLHDE-RGPVLEALIARTIRNIEATQEDVRLVGLSATLPNYKDVATLLRIKPETGL 873
DEIHLL D RGPVLE+++AR R E +R+VGLSATLPN ++VA L K
Sbjct: 153 DEIHLLGDRTRGPVLESIVARMRR----LNELIRIVGLSATLPNAEEVADWLNAKLVESD 208
Query: 874 FYFDNSFRPVALEQQYIGVTEKKALKRFQVMNDIVYEKVMEHAGRN-QLLVFVHSRKETG 932
+ R V ++G KK +++++ E V+E Q+LVFVHSRKE
Sbjct: 209 WRPVPLRRGVPYVGAFLGADGKKK-TWPLLIDNLALELVLESLAEGGQVLVFVHSRKEAE 267
Query: 933 KTARAIRDMCLEKDTLGQFLREGSASMEVLRTEADQVKNGELRDLLPYGFAIHHAGMTRV 992
KTA+ +R + + + + +L E ++ EL +L+ G A HHAG+ R
Sbjct: 268 KTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPRE 327
Query: 993 DRTLVEDLFADRHIQVLVSTATLAWGVNLPAHTVVDRTLVEDLFADRHIQVLVSTATLAW 1052
DR LVED F I+VLVST TLA
Sbjct: 328 DRQLVEDAFRKGKIKVLVSTPTLAA----------------------------------- 352
Query: 1053 GVNLPAHTVIIKGTQIYNPEKGRWVELGALDVLQMLGRAGRPQYDTKGEGVLITN-HSEL 1111
GVNLPA TVIIK T+ Y+P+ G V++ LDVLQM GRAGRP YD GE +++ H EL
Sbjct: 353 GVNLPARTVIIKDTRRYDPKGG-IVDIPVLDVLQMAGRAGRPGYDDYGEAIILATSHDEL 411
Query: 1112 QYYLSLLNHQLPVESQMISKLPDMLNAEIVLGTVQNLKDAVTWLGYTYLYIRMLRAPNLY 1171
+Y L P + SKL D LN L V ++ DAV+WL T Y R P Y
Sbjct: 412 EYLAELYIQSEPEPIE--SKLGDELNLRTFLLGVISVGDAVSWLELTDFYERTFYNPQTY 469
Query: 1172 GISHDALKEDPLLECHRADLIHTAALHLERSGLIKYDRKSGHMQVTELGRIASHYYCTHE 1231
G + L +LE +GLI D + TELG++ S Y E
Sbjct: 470 GEGMLREEILASLR------------YLEENGLI-LDADWEALHATELGKLVSRLYIDPE 516
Query: 1232 TMATYNQLLK---PTLSEIELFRVFSLSGEFRHITVREEEKLELQK--LMERAPIPIKES 1286
+ + LL +EI L + SL+ + I +RE E EL L E++ + E
Sbjct: 517 SAKIFRDLLAELALEPTEIGLLYLISLTPDLMPIKLRERESSELVLDELEEQSDYLLGER 576
Query: 1287 TDEPSAKVNILLQAYISQLKLEGFALMSDMVFVTQSAARLMRAIFEIVLYRGWAQLADKA 1346
DE + + N+LLQA + +L + +D + + + I W L+
Sbjct: 577 LDELAVEYNLLLQALKTAARLLDWINEADEDEILNAYGVAPGDLLRIAETAEW--LSADL 634
Query: 1347 LSLCKMVDRRMWQSMSPLRQFRKIPEEIIKKIEKKNFPWERLYDLGPNEIGELIRVPKLG 1406
L+L K +R L RK E + +IE E L +L +R KL
Sbjct: 635 LALGKAAERLAKILGLGLHVLRK-LEILSLRIEYGVRS-EELLELVEIRGVGRVRARKLY 692
Query: 1407 KTIHKYVHQFPKLELATHIQPITRSTLRVELTISPDFQWDEKLHGGSEGFWILVEDVDSE 1466
+K + + + P+T R+ I D L G + F I V ++D
Sbjct: 693 NAGYKSLEDLRLIADPAELLPLTGIGERLVEAILESLGRDVLLSGRAYFFSIEVRELDLL 752
Query: 1467 AI 1468
+
Sbjct: 753 YV 754
Score = 120 bits (302), Expect = 3e-27
Identities = 61/278 (21%), Positives = 105/278 (37%), Gaps = 75/278 (26%)
Query: 445 EVHVPA--LKPKPMGPDETLVPIDKLPRYVQHAFEDFKTLNRIQSRLCKSALESDENLLL 502
E+ + L + D+ ++ I K + N Q + + L SDEN+L+
Sbjct: 1 EIFMKEEKLATSKVKLDDRVLEILKGDGIDE-------LFNPQQEAV-EKGLLSDENVLI 52
Query: 503 CAPTGAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPMRSLVQEMVGNFGKDE-- 560
APTG+GKT +ALL +L + + K++Y+ P+++L +E F + E
Sbjct: 53 SAPTGSGKTLIALLAILSTLLEG----------GGKVVYIVPLKALAEEKYEEFSRLEEL 102
Query: 561 ---IHLLHDERGPVLEALIART-------------IRNIEATQEDVRLV----------- 593
+ + + + + +AR R + E+V LV
Sbjct: 103 GIRVGISTGDY-DLDDERLARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDR 161
Query: 594 -----------------------GLSATLPNYKDVATLLRIKPETGLFYFDNSFRPVALE 630
GLSATLPN ++VA L K + R V
Sbjct: 162 TRGPVLESIVARMRRLNELIRIVGLSATLPNAEEVADWLNAKLVESDWRPVPLRRGVPYV 221
Query: 631 QQYIGVTEKKALKRFQVMNDIVYEKVMEHAGRN-QLLV 667
++G KK +++++ E V+E Q+LV
Sbjct: 222 GAFLGADGKKK-TWPLLIDNLALELVLESLAEGGQVLV 258
Score = 30.8 bits (70), Expect = 7.3
Identities = 14/46 (30%), Positives = 19/46 (41%)
Query: 668 STLRVELTISPDFQWDEKLHGGSEGFWILVEDVDSEVVLHHEYFLL 713
R+ I D L G + F I V ++D VLH E +L
Sbjct: 717 IGERLVEAILESLGRDVLLSGRAYFFSIEVRELDLLYVLHEEALIL 762
>gnl|CDD|217270 pfam02889, Sec63, Sec63 Brl domain. This domain (also known as the
Brl domain) is required for assembly of functional
endoplasmic reticulum translocons.
Length = 309
Score = 351 bits (903), Expect = e-110
Identities = 139/256 (54%), Positives = 187/256 (73%), Gaps = 4/256 (1%)
Query: 1217 TELGRIASHYYCTHETMATYNQLLKPTLSEIELFRVFSLSGEFRHITVREEEKLELQKLM 1276
TELGRIASHYY +ETM T+N LKP + +L + S + EF I VREEEK EL+KL+
Sbjct: 2 TELGRIASHYYILYETMETFNTSLKPNTTLKDLLEILSSASEFEEIPVREEEKKELKKLL 61
Query: 1277 ERAPIPIKEST-DEPSAKVNILLQAYISQLKLEGFALMSDMVFVTQSAARLMRAIFEIVL 1335
ER PIP+K + D+P AKVN+LLQAY+S+LKL F+L+SD+ ++ Q+A RL+RA+FEI L
Sbjct: 62 ERVPIPVKSPSIDDPHAKVNLLLQAYLSRLKLPDFSLVSDLNYILQNAGRLLRALFEIAL 121
Query: 1336 YRGWAQLADKALSLCKMVDRRMWQSMSPLRQFRKIPEEIIKKIEKKN-FPWERLYDLGPN 1394
+GW A AL L KM+++R+W S SPLRQ IP E++KK+EKK E L DL P
Sbjct: 122 SKGWLSPALNALELSKMIEQRLWPSDSPLRQLPHIPPEVLKKLEKKGISSLEDLMDLDPE 181
Query: 1395 EIGELIRV-PKLGKTIHKYVHQFPKLELATHIQPITRS-TLRVELTISPDFQWDEKLHGG 1452
E+GEL+ PK GK I ++V++FP+LE+ +QPITR +LRVE+T++ DF+WDE+ HG
Sbjct: 182 ELGELLGNNPKQGKDIAEFVNRFPRLEIEAEVQPITREVSLRVEVTLTRDFEWDERFHGK 241
Query: 1453 SEGFWILVEDVDSEAI 1468
SEGFWI+VED D+ +
Sbjct: 242 SEGFWIVVEDSDNNEL 257
Score = 224 bits (574), Expect = 1e-65
Identities = 76/210 (36%), Positives = 121/210 (57%), Gaps = 13/210 (6%)
Query: 1467 AIRLIQACVDVLSSNGWLSPAVAAMEVAQMITQAMWSKDSYLKQLPHFNADIIKRCTEKG 1526
A RL++A ++ S GWLSPA+ A+E+++MI Q +W DS L+QLPH +++K+ +KG
Sbjct: 109 AGRLLRALFEIALSKGWLSPALNALELSKMIEQRLWPSDSPLRQLPHIPPEVLKKLEKKG 168
Query: 1527 VETVFDIMELEDDDRLRLLQLSESQLADVARFCNRYPNIELSYEVLNKDRISSGSSVNVV 1586
+ ++ D+M+L+ ++ LL + Q D+A F NR+P +E+ EV R S+ V
Sbjct: 169 ISSLEDLMDLDPEELGELLGNNPKQGKDIAEFVNRFPRLEIEAEVQPITR---EVSLRVE 225
Query: 1587 VNLDREDEVTGPVIAPFYPQKREEGWWVVIGDPKTNSLLSIKRLTLQQKAK-IKLDFVAP 1645
V L R+ E + K EG+W+V+ D N LL+I+R TL +K +L+F P
Sbjct: 226 VTLTRDFE-----WDERFHGK-SEGFWIVVEDSDNNELLAIERFTLNKKKDEHELEFTVP 279
Query: 1646 NPGHH---SYALYFMSDAYLGCDQEYKFSI 1672
G + +SD++LGCDQE S+
Sbjct: 280 LSGGPLPPQLTIRLVSDSWLGCDQEVPVSL 309
Score = 110 bits (278), Expect = 3e-26
Identities = 44/91 (48%), Positives = 62/91 (68%), Gaps = 3/91 (3%)
Query: 669 TLRVELTISPDFQWDEKLHGGSEGFWILVEDVDSEVVLHHEYFLLKSRYATDDHVVKFFV 728
+LRVE+T++ DF+WDE+ HG SEGFWI+VED D+ +L E F L + H ++F V
Sbjct: 221 SLRVEVTLTRDFEWDERFHGKSEGFWIVVEDSDNNELLAIERFTLNKKKDE--HELEFTV 278
Query: 729 PVF-EPLPPQYFLRIVSDRWIGAETILPVSF 758
P+ PLPPQ +R+VSD W+G + +PVS
Sbjct: 279 PLSGGPLPPQLTIRLVSDSWLGCDQEVPVSL 309
>gnl|CDD|214744 smart00611, SEC63, Domain of unknown function in Sec63p, Brr2p and
other proteins.
Length = 312
Score = 327 bits (840), Expect = e-101
Identities = 111/259 (42%), Positives = 173/259 (66%), Gaps = 3/259 (1%)
Query: 1213 HMQVTELGRIASHYYCTHETMATYNQLLKPTLSEIELFRVFSLSGEFRHITVREEEKLEL 1272
+ T+LGRIAS+YY ++ T+ T+N+LLKP ++ +L R+ S+S EF I VR EE L L
Sbjct: 1 GIWPTDLGRIASYYYISYTTIRTFNELLKPKMTTKDLLRILSMSSEFDQIPVRHEEDLLL 60
Query: 1273 QKLMERAPIPIK-ESTDEPSAKVNILLQAYISQLKLEGFALMSDMVFVTQSAARLMRAIF 1331
++L E+ PI ++ S D+P K N+LLQA++S+LKL FAL SD V+V Q+A RL++A+
Sbjct: 61 EELAEKLPIRLENPSLDDPHVKANLLLQAHLSRLKLPSFALESDTVYVLQNAGRLLQAMV 120
Query: 1332 EIVLYRGWAQLADKALSLCKMVDRRMWQSMSPLRQFRKIPEEIIKKIEKKN-FPWERLYD 1390
+I L RGW A AL+L +M+ + +W + SPL Q +PEEI+K++EKK E L +
Sbjct: 121 DIALERGWLSTALNALNLSQMIIQALWPTDSPLLQLPHLPEEILKRLEKKKVLSLEDLLE 180
Query: 1391 LGPNEIGELIRVP-KLGKTIHKYVHQFPKLELATHIQPITRSTLRVELTISPDFQWDEKL 1449
L E GEL+ + G+ ++K + + PKL + ++PITR+ L VE+T++ D WD+++
Sbjct: 181 LEDEERGELLGLLDAEGERVYKVLSRLPKLNIEISLEPITRTVLGVEVTLTVDLTWDDEI 240
Query: 1450 HGGSEGFWILVEDVDSEAI 1468
HG EG+W+++ D D +
Sbjct: 241 HGKQEGWWLVIGDSDGNEL 259
Score = 236 bits (605), Expect = 9e-70
Identities = 87/211 (41%), Positives = 126/211 (59%), Gaps = 14/211 (6%)
Query: 1467 AIRLIQACVDVLSSNGWLSPAVAAMEVAQMITQAMWSKDSYLKQLPHFNADIIKRCTEKG 1526
A RL+QA VD+ GWLS A+ A+ ++QMI QA+W DS L QLPH +I+KR +K
Sbjct: 112 AGRLLQAMVDIALERGWLSTALNALNLSQMIIQALWPTDSPLLQLPHLPEEILKRLEKKK 171
Query: 1527 VETVFDIMELEDDDRLRLLQLSESQLADVARFCNRYPNIELSYEVLNKDRISSGSSVNVV 1586
V ++ D++ELED++R LL L +++ V + +R P + + + R G V +
Sbjct: 172 VLSLEDLLELEDEERGELLGLLDAEGERVYKVLSRLPKLNIEISLEPITRTVLGVEVTLT 231
Query: 1587 VNLDREDEVTGPVIAPFYPQKREEGWWVVIGDPKTNSLLSIKRLTLQQKAK---IKLDFV 1643
V+L +DE+ G ++EGWW+VIGD N LL I+R +L +K +KLDF
Sbjct: 232 VDLTWDDEIHG----------KQEGWWLVIGDSDGNELLHIERFSLNKKNVSEEVKLDFT 281
Query: 1644 AP-NPGHHSYALYFMSDAYLGCDQEYKFSID 1673
AP G++ Y L +SD+YLGCDQEY S D
Sbjct: 282 APATEGNYQYTLRLVSDSYLGCDQEYPLSFD 312
Score = 108 bits (273), Expect = 2e-25
Identities = 37/121 (30%), Positives = 63/121 (52%), Gaps = 9/121 (7%)
Query: 639 KKALKRFQVMNDIVYEKVMEHAGRNQLLVSTLRVELTISPDFQWDEKLHGGSEGFWILVE 698
K L R +N + + + + L VE+T++ D WD+++HG EG+W+++
Sbjct: 201 YKVLSRLPKLNIEISLEPITR--------TVLGVEVTLTVDLTWDDEIHGKQEGWWLVIG 252
Query: 699 DVDSEVVLHHEYFLLKSRYATDDHVVKFFVPVFEPLPPQYFLRIVSDRWIGAETILPVSF 758
D D +LH E F L + +++ + F P E QY LR+VSD ++G + P+SF
Sbjct: 253 DSDGNELLHIERFSLNKKNVSEEVKLDFTAPATEGN-YQYTLRLVSDSYLGCDQEYPLSF 311
Query: 759 R 759
Sbjct: 312 D 312
>gnl|CDD|214946 smart00973, Sec63, Sec63 Brl domain. This domain was named after the
yeast Sec63 (or NPL1) (also known as the Brl domain)
protein in which it was found. This protein is required
for assembly of functional endoplasmic reticulum
translocons. Other yeast proteins containing this domain
include pre-mRNA splicing helicase BRR2, HFM1 protein and
putative helicases.
Length = 314
Score = 288 bits (739), Expect = 1e-87
Identities = 116/266 (43%), Positives = 172/266 (64%), Gaps = 8/266 (3%)
Query: 1217 TELGRIASHYYCTHETMATYNQLLKPTLSEIELFRVFSLSGEFRHITVREEEKLELQKLM 1276
TELGRIAS+YY ++ET+ T+NQ LKPT + ++ + S + EF+ I VR EK EL +L
Sbjct: 2 TELGRIASYYYISYETIETFNQSLKPTTTLKDILEILSRASEFKEIPVRHNEKKELNELN 61
Query: 1277 ERAPIPIKES-TDEPSAKVNILLQAYISQLKLEGFALMSDMVFVTQSAARLMRAIFEIVL 1335
+R PIP+KE D P AKVN+LLQA++S+L L F L+SD+ ++ Q+A R++RA+ +I L
Sbjct: 62 KRVPIPVKEGIIDSPHAKVNLLLQAHLSRLPLPDFDLVSDLKYILQNAPRILRALVDIAL 121
Query: 1336 YRGWAQLADKALSLCKMVDRRMW-QSMSPLRQFRKI-PEEIIKKIEKKNFPW--ERLYDL 1391
+GW + A AL L +MV +R+W S SPL+Q E++ K+E K+ E L D+
Sbjct: 122 SKGWLRTALNALDLSQMVVQRLWEDSDSPLKQLPHFLIEDVYDKLELKDGSRSFELLLDM 181
Query: 1392 GPNEIGELI-RVPKLGKTIHKYVHQFPKLELATHIQPITRS-TLRVELTISPDFQWDEK- 1448
E+GE + R+P G+ I++ + +FPK+E+ + PITR TLRVEL I+P F WD
Sbjct: 182 NAAELGEFLNRLPPNGRLIYELLRRFPKIEVEAEVLPITRDLTLRVELEITPVFAWDLPR 241
Query: 1449 LHGGSEGFWILVEDVDSEAIRLIQAC 1474
G SE +W++V D D+ + I+
Sbjct: 242 HKGKSESWWLVVGDSDTNELLAIKRV 267
Score = 187 bits (478), Expect = 1e-52
Identities = 86/218 (39%), Positives = 124/218 (56%), Gaps = 24/218 (11%)
Query: 1467 AIRLIQACVDVLSSNGWLSPAVAAMEVAQMITQAMWS-KDSYLKQLPHFNADIIKRCTEK 1525
A R+++A VD+ S GWL A+ A++++QM+ Q +W DS LKQLPHF
Sbjct: 109 APRILRALVDIALSKGWLRTALNALDLSQMVVQRLWEDSDSPLKQLPHF----------- 157
Query: 1526 GVETVFDIMELEDDDRLRLLQLSESQLADVARFCNR-YPNIELSYEVLNKD--RISSGSS 1582
+E V+D +EL+D R L L + A++ F NR PN L YE+L +
Sbjct: 158 LIEDVYDKLELKDGSRSFELLL-DMNAAELGEFLNRLPPNGRLIYELLRRFPKIEVEAEV 216
Query: 1583 VNVVVNLDREDEVT-GPVIAPFYPQ--KREEGWWVVIGDPKTNSLLSIKRLTLQQKAK-- 1637
+ + +L E+ PV A P+ + E WW+V+GD TN LL+IKR+TL++K K
Sbjct: 217 LPITRDLTLRVELEITPVFAWDLPRHKGKSESWWLVVGDSDTNELLAIKRVTLRKKKKSN 276
Query: 1638 -IKLDFVAP--NPGHHSYALYFMSDAYLGCDQEYKFSI 1672
+KLDF P PG +Y +Y +SD+YLGCDQE FS+
Sbjct: 277 EVKLDFTVPLSEPGPENYTVYLISDSYLGCDQEVSFSL 314
Score = 102 bits (257), Expect = 2e-23
Identities = 31/91 (34%), Positives = 52/91 (57%), Gaps = 1/91 (1%)
Query: 669 TLRVELTISPDFQWDEK-LHGGSEGFWILVEDVDSEVVLHHEYFLLKSRYATDDHVVKFF 727
TLRVEL I+P F WD G SE +W++V D D+ +L + L+ + +++ + F
Sbjct: 224 TLRVELEITPVFAWDLPRHKGKSESWWLVVGDSDTNELLAIKRVTLRKKKKSNEVKLDFT 283
Query: 728 VPVFEPLPPQYFLRIVSDRWIGAETILPVSF 758
VP+ EP P Y + ++SD ++G + + S
Sbjct: 284 VPLSEPGPENYTVYLISDSYLGCDQEVSFSL 314
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 127 bits (321), Expect = 7e-30
Identities = 122/437 (27%), Positives = 190/437 (43%), Gaps = 102/437 (23%)
Query: 809 VGNFGKDEIHLLHDE-RGPVLEALIARTIRNIEATQEDVRLVGLSATLPNYKDVATLLRI 867
VG DEIH++ DE RGP LE +++ + R + D R++ LSAT+ N ++A L
Sbjct: 136 VGLIVADEIHIIGDEDRGPTLETVLS-SARYVNP---DARILALSATVSNANELAQWLNA 191
Query: 868 KPETGLFYFDNSFRPVALEQQYIGVTEKKAL-----KRFQVMNDIVYEKVMEHAGRNQLL 922
++FRPV L+ +G+ +K L +R QV + + ++ + G Q+L
Sbjct: 192 S------LIKSNFRPVPLK---LGILYRKRLILDGYERSQVDINSLIKETVNDGG--QVL 240
Query: 923 VFVHSRKETGKTARAIRDMCLEKDTLGQFLREGSASMEVLRTEADQVKNGELRDLLPYGF 982
VFV SRK A L Q E +V + V + L ++LP+G
Sbjct: 241 VFVSSRKNAEDYAE----------MLIQHFPE-FNDFKVSSENNN-VYDDSLNEMLPHGV 288
Query: 983 AIHHAGMTRVDRTLVEDLFADRHIQVLVSTATLAWGVNLPAHTVVDRTLVEDLFADRHIQ 1042
A HHAG++ R +E++F R+ R+I+
Sbjct: 289 AFHHAGLSNEQRRFIEEMF--RN---------------------------------RYIK 313
Query: 1043 VLVSTATLAWGVNLPAHTVIIKGTQIYNPEKGRWVELGALDVLQMLGRAGRPQYDTKGEG 1102
V+V+T TLA GVNLPA VI++ Y R+ L +++ QM+GRAGRP YD G G
Sbjct: 314 VIVATPTLAAGVNLPARLVIVRDITRYGNGGIRY--LSNMEIKQMIGRAGRPGYDQYGIG 371
Query: 1103 VLITNHSELQY-----YLSLLNHQLPVESQMISKLPDMLN--AEIVLGTVQNLKDAVTWL 1155
I S Y YLS PV S M S+ N A I +G +++D + +
Sbjct: 372 -YIYAASPASYDAAKKYLS--GEPEPVISYMGSQRKVRFNTLAAISMGLASSMEDLILFY 428
Query: 1156 GYTYLYIRMLRAPNLYGISHDALKEDPLLECHRADLIHTAALHLERSGLIKYDRKSGHMQ 1215
T + I+ ++ I ++ L+ +G IK ++
Sbjct: 429 NETLMAIQ---------------NGVDEID----YYIESSLKFLKENGFIK---GDVTLR 466
Query: 1216 VTELGRIASHYYCTHET 1232
T LG++ S Y E+
Sbjct: 467 ATRLGKLTSDLYIDPES 483
Score = 48.7 bits (116), Expect = 3e-05
Identities = 54/236 (22%), Positives = 93/236 (39%), Gaps = 84/236 (35%)
Query: 494 LESDENLLLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPMRSLVQE-- 551
L EN+++ PT AGKT +A + + + K IY+ P+RSL E
Sbjct: 34 LRKGENVIVSVPTAAGKTLIAYSAIYETFLAGL-----------KSIYIVPLRSLAMEKY 82
Query: 552 -------------------------------------------------MVGNFGK---D 559
++ + G D
Sbjct: 83 EELSRLRSLGMRVKISIGDYDDPPDFIKRYDVVILTSEKADSLIHHDPYIINDVGLIVAD 142
Query: 560 EIHLLHDE-RGPVLEALIARTIRNIEATQEDVRLVGLSATLPNYKDVATLLRIKPETGLF 618
EIH++ DE RGP LE +++ + R + D R++ LSAT+ N ++A L
Sbjct: 143 EIHIIGDEDRGPTLETVLS-SARYVNP---DARILALSATVSNANELAQWLNAS------ 192
Query: 619 YFDNSFRPVALEQQYIGVTEKKAL-----KRFQVMNDIVYEKVMEHAGRNQLLVST 669
++FRPV L+ +G+ +K L +R QV + + ++ + G+ + VS+
Sbjct: 193 LIKSNFRPVPLK---LGILYRKRLILDGYERSQVDINSLIKETVNDGGQVLVFVSS 245
>gnl|CDD|235032 PRK02362, PRK02362, ski2-like helicase; Provisional.
Length = 737
Score = 116 bits (292), Expect = 4e-26
Identities = 99/322 (30%), Positives = 137/322 (42%), Gaps = 88/322 (27%)
Query: 815 DEIHLLHDE-RGPVLEALIARTIRNIEATQEDVRLVGLSATLPNYKDVATLLR------- 866
DE+HL+ RGP LE +A+ R Q +V LSAT+ N ++A L
Sbjct: 144 DEVHLIDSANRGPTLEVTLAKLRRLNPDLQ----VVALSATIGNADELADWLDAELVDSE 199
Query: 867 ---IKPETGLFY-----FDNSFRPVALEQQYIGVTEKKALKRFQVMNDIVYEKVMEHAGR 918
I G+FY FD+S R V + + +N +V + + E
Sbjct: 200 WRPIDLREGVFYGGAIHFDDSQREVEVPSKD------------DTLN-LVLDTLEEGG-- 244
Query: 919 NQLLVFVHSRKE----TGKTARAIRDMCLEKDTLGQFLREGSASM--EVLRT-EADQVKN 971
Q LVFV SR+ + A A+ K TL R A + E+ + + K+
Sbjct: 245 -QCLVFVSSRRNAEGFAKRAASAL------KKTLTAAERAELAELAEEIREVSDTETSKD 297
Query: 972 GELRDLLPYGFAIHHAGMTRVDRTLVEDLFADRHIQVLVSTATLAWGVNLPAHTVVDRTL 1031
L D + G A HHAG++R H R L
Sbjct: 298 --LADCVAKGAAFHHAGLSR-------------------------------EH----REL 320
Query: 1032 VEDLFADRHIQVLVSTATLAWGVNLPAHTVIIKGTQIYNPEKGRWVELGALDVLQMLGRA 1091
VED F DR I+V+ ST TLA G+NLPA VII+ + Y+ G + L+ QM GRA
Sbjct: 321 VEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGM-QPIPVLEYHQMAGRA 379
Query: 1092 GRPQYDTKGEGVLIT-NHSELQ 1112
GRP D GE VL+ ++ EL
Sbjct: 380 GRPGLDPYGEAVLLAKSYDELD 401
Score = 44.6 bits (106), Expect = 4e-04
Identities = 49/201 (24%), Positives = 69/201 (34%), Gaps = 85/201 (42%)
Query: 498 ENLLLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPMRSLVQE------ 551
+NLL PT +GKT +A L ML K I G K +Y+ P+R+L E
Sbjct: 40 KNLLAAIPTASGKTLIAELAML----KAIARGG-------KALYIVPLRALASEKFEEFE 88
Query: 552 -----------MVGNFGKDE-------------------------------------IHL 563
G++ + +HL
Sbjct: 89 RFEELGVRVGISTGDYDSRDEWLGDNDIIVATSEKVDSLLRNGAPWLDDITCVVVDEVHL 148
Query: 564 LHDE-RGPVLEALIARTIRNIEATQEDVRLVGLSATLPNYKDVATLLR----------IK 612
+ RGP LE +A+ R Q +V LSAT+ N ++A L I
Sbjct: 149 IDSANRGPTLEVTLAKLRRLNPDLQ----VVALSATIGNADELADWLDAELVDSEWRPID 204
Query: 613 PETGLFY-----FDNSFRPVA 628
G+FY FD+S R V
Sbjct: 205 LREGVFYGGAIHFDDSQREVE 225
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 103 bits (258), Expect = 4e-22
Identities = 89/306 (29%), Positives = 145/306 (47%), Gaps = 71/306 (23%)
Query: 815 DEIHLLHD-ERGPVLEALIARTIRNIEATQEDVRLVGLSATLPNYKDVATLLRIKPETGL 873
DEIHL+ +RG LE ++ + +++GLSAT+ N +++A L +
Sbjct: 145 DEIHLIGSYDRGATLEMILTHML-------GRAQILGLSATVGNAEELAEWLNAE----- 192
Query: 874 FYFDNSFRPVALEQQ--YIGVT--EKKALKRFQV-MNDIVYEKVMEHAGRNQLLVFVHSR 928
+ +RPV L + Y G E ++RF +VY+ V + G LVFV++R
Sbjct: 193 -LVVSDWRPVKLRKGVFYQGFLFWEDGKIERFPNSWESLVYDAVKKGKGA---LVFVNTR 248
Query: 929 KETGKTA----RAIRDMCLEKDTLGQFLREGSASMEVLRTEADQVKNGELRDLLPYGFAI 984
+ K A + I+ + + L+E + S+E + N +L+ L G A
Sbjct: 249 RSAEKEALELAKKIKRFLTKPELRA--LKELADSLE------ENPTNEKLKKALRGGVAF 300
Query: 985 HHAGMTRVDRTLVEDLFADRHIQVLVSTATLAWGVNLPAHTVVDRTLVEDLFADRHIQVL 1044
HHAG+ R +R L+ED F + G+ I+V+
Sbjct: 301 HHAGLGRTERVLIEDAFRE--------------GL---------------------IKVI 325
Query: 1045 VSTATLAWGVNLPAHTVIIKGTQIYNPEKGRWVELGALDVLQMLGRAGRPQYDTKGEGVL 1104
+T TL+ G+NLPA VII+ T+ Y+ G W ++ L++ QM+GRAGRP+YD GE ++
Sbjct: 326 TATPTLSAGINLPAFRVIIRDTKRYS-NFG-WEDIPVLEIQQMMGRAGRPKYDEVGEAII 383
Query: 1105 ITNHSE 1110
+ E
Sbjct: 384 VATTEE 389
Score = 32.9 bits (75), Expect = 1.6
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 10/71 (14%)
Query: 486 QSRLCKSALESDENLLLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPM 545
Q+ KS + +NL+L PT +GKT VA + M+ ++ + G K +Y+ P+
Sbjct: 28 QAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKL---LREGG-------KAVYLVPL 77
Query: 546 RSLVQEMVGNF 556
++L +E F
Sbjct: 78 KALAEEKYREF 88
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific [General
function prediction only].
Length = 830
Score = 90.2 bits (224), Expect = 5e-18
Identities = 78/298 (26%), Positives = 115/298 (38%), Gaps = 100/298 (33%)
Query: 815 DEIHLLHD-ERGPVLEALIARTIRNIEATQEDVRLVGLSATLPNYKDVATLLRIKPETGL 873
DEIH L D ERGP L+ LI R + + + LSAT+ N +++A L K L
Sbjct: 345 DEIHTLEDEERGPRLDGLIGR----LRYLFPGAQFIYLSATVGNPEELAKKLGAK----L 396
Query: 874 FYFDNSFRPVALEQQYI---GVTEKKALKRFQVMNDIVYEKVMEHAG---RNQLLVFVHS 927
+D RPV LE+ + +EK + + +V + + R Q +VF +S
Sbjct: 397 VLYDE--RPVPLERHLVFARNESEKWDI-----IARLVKREFSTESSKGYRGQTIVFTYS 449
Query: 928 RKETGKTARAIRDMCLEKDTLGQFLREGSASMEVLRTEADQVKNGELRDLLPYGFAIHHA 987
R+ + A A+ G+ PY HA
Sbjct: 450 RRRCHELADAL--------------------------------TGKGLKAAPY-----HA 472
Query: 988 GMTRVDRTLVEDLFADRHIQVLVSTATLAWGVNLPAHTVVDRTLVEDLFADRHIQVLVST 1047
G+ +R VE FA + + +V+TA LA GV+ PA V+
Sbjct: 473 GLPYKERKSVERAFAAQELAAVVTTAALAAGVDFPASQVI-------------------F 513
Query: 1048 ATLAWGVNLPAHTVIIKGTQIYNPEKGRWVELGALDVLQMLGRAGRPQYDTKGEGVLI 1105
+LA G+ W L + QMLGRAGRP Y +G+ L+
Sbjct: 514 ESLAMGI--------------------EW--LSVREFQQMLGRAGRPDYHDRGKVYLL 549
Score = 45.9 bits (109), Expect = 2e-04
Identities = 29/77 (37%), Positives = 40/77 (51%), Gaps = 11/77 (14%)
Query: 559 DEIHLLHD-ERGPVLEALIARTIRNIEATQEDVRLVGLSATLPNYKDVATLLRIKPETGL 617
DEIH L D ERGP L+ LI R + + + LSAT+ N +++A L K L
Sbjct: 345 DEIHTLEDEERGPRLDGLIGR----LRYLFPGAQFIYLSATVGNPEELAKKLGAK----L 396
Query: 618 FYFDNSFRPVALEQQYI 634
+D RPV LE+ +
Sbjct: 397 VLYDE--RPVPLERHLV 411
Score = 33.6 bits (77), Expect = 1.1
Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 4/68 (5%)
Query: 459 DETLVPIDKL--PRYVQHAFED--FKTLNRIQSRLCKSALESDENLLLCAPTGAGKTNVA 514
+ VP+D+L P + + + L +Q ++ L ENLL+ + T +GKT +
Sbjct: 190 EVERVPVDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIG 249
Query: 515 LLCMLQEI 522
L + +
Sbjct: 250 ELAGIPRL 257
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 76.7 bits (189), Expect = 9e-14
Identities = 92/389 (23%), Positives = 143/389 (36%), Gaps = 108/389 (27%)
Query: 815 DEIHLLHD-ERGPVLEALIARTIRNIEATQEDVRLVGLSATLPNYKDVATLL-RIKPETG 872
DE+H + D ERG V E +I I VR V LSAT+PN ++ A + R+ +
Sbjct: 236 DEVHYIGDRERGVVWEEVI------ILLPD-HVRFVFLSATVPNAEEFAEWIQRVHSQPI 288
Query: 873 LFYFDNSFRPVALEQQYIG-------VTEKK---------ALKRFQVMNDIVYE------ 910
RPV LE V EKK A + ++ V E
Sbjct: 289 HVVSTE-HRPVPLEHFVYVGKGLFDLVDEKKKFNAENFPSANRSLSCFSEKVRETDDGDV 347
Query: 911 ---------------------KVMEHAGRNQLL---VFVHSRKETGKTARAI--RDMCLE 944
+++ ++ LL VF SR+ + A+ + D+ L
Sbjct: 348 GRYARRTKALRGSAKGPAGRPEIVNKLDKDNLLPAIVFSFSRRGCEEAAQILSTLDLVLT 407
Query: 945 KDTLGQFLREGSASMEVLRTEADQVKNG--ELRDLLPYGFAIHHAGMTRVDRTLVEDLFA 1002
++ ++ L E ++ E+ LL G A+HHAG+ + LVE+LF
Sbjct: 408 EEKERAIREIIDHAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLPAIKELVEELFQ 467
Query: 1003 DRHIQVLVSTATLAWGVNLPAHTVVDRTLVEDLFADRHIQVLVSTATLAWGVNLPAHTVI 1062
+ ++V+ +T T A G+N+PA TVV +L +
Sbjct: 468 EGLVKVVFATETFAIGINMPARTVVFTSLSK----------------------------- 498
Query: 1063 IKGTQIYNPEKGRWVELGALDVLQMLGRAGRPQYDTKGEGVLITNHSELQYYLSLLNHQL 1122
G RW+ G QM GRAGR D G ++I E +
Sbjct: 499 FDGNGH------RWLSPGEY--TQMSGRAGRRGLDVLGTVIVIEPPFESEP--------- 541
Query: 1123 PVESQMISKLPDMLNAEIVL--GTVQNLK 1149
+ + S D L ++ L + NL
Sbjct: 542 SEAAGLASGKLDPLRSQFRLSYNMILNLL 570
Score = 54.7 bits (132), Expect = 4e-07
Identities = 53/206 (25%), Positives = 77/206 (37%), Gaps = 73/206 (35%)
Query: 481 TLNRIQSRLCKSALESDENLLLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFKII 540
L+ Q + LE E++L+CAPT +GKT VA + + DG ++I
Sbjct: 119 ELDPFQQEAI-AILERGESVLVCAPTSSGKTVVAEYAIALAL-----RDGQ------RVI 166
Query: 541 YVAPMRSL--------------VQEMVG-----------------------NFGK----- 558
Y +P+++L V +MVG N
Sbjct: 167 YTSPIKALSNQKYRDLLAKFGDVADMVGLMTGDVSINPDAPCLVMTTEILRNMLYRGSES 226
Query: 559 ---------DEIHLLHD-ERGPVLEALIARTIRNIEATQEDVRLVGLSATLPNYKDVATL 608
DE+H + D ERG V E +I I VR V LSAT+PN ++ A
Sbjct: 227 LRDIEWVVFDEVHYIGDRERGVVWEEVI------ILLPD-HVRFVFLSATVPNAEEFAEW 279
Query: 609 L-RIKPETGLFYFDNSFRPVALEQQY 633
+ R+ + RPV LE
Sbjct: 280 IQRVHSQPIHVVSTE-HRPVPLEHFV 304
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 60.7 bits (148), Expect = 2e-10
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 9/76 (11%)
Query: 483 NRIQSRLCKSALESDENLLLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFKIIYV 542
IQ++ + L +++L+ APTG+GKT LL +LQ + + + +
Sbjct: 1 TPIQAQAIPAILS-GKDVLVQAPTGSGKTLAFLLPILQALLP--------KKGGPQALVL 51
Query: 543 APMRSLVQEMVGNFGK 558
AP R L +++ K
Sbjct: 52 APTRELAEQIYEELKK 67
Score = 41.9 bits (99), Expect = 6e-04
Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 8/52 (15%)
Query: 763 GAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPMRSLVQEMVGNFGK 814
G+GKT LL +LQ + + + +AP R L +++ K
Sbjct: 24 GSGKTLAFLLPILQALLP--------KKGGPQALVLAPTRELAEQIYEELKK 67
Score = 35.7 bits (83), Expect = 0.080
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 9/49 (18%)
Query: 815 DEIHLLHD-ERGPVLEALIARTIRNIEATQEDVRLVGLSATLP-NYKDV 861
DE H L D G LE +++R D +++ LSATLP N +D+
Sbjct: 128 DEAHRLLDMGFGDDLEEILSRL-------PPDRQILLLSATLPRNLEDL 169
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 54.9 bits (133), Expect = 3e-09
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 978 LPYGFAIHHAGMTRVDRTLVEDLFADRHIQVLVSTATLAWGVNLP-AHTVVD 1028
L A H G+++ +R + D F + I+VLV+T G++LP V+
Sbjct: 10 LGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVII 61
Score = 54.1 bits (131), Expect = 5e-09
Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 12/68 (17%)
Query: 1028 DRTLVEDLFADRHIQVLVSTATLAWGVNLP-AHTVIIKGTQIYNPEKGRWVELGALDVLQ 1086
+R + D F + I+VLV+T G++LP VII +P +Q
Sbjct: 25 EREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPW-SPA----------SYIQ 73
Query: 1087 MLGRAGRP 1094
+GRAGR
Sbjct: 74 RIGRAGRA 81
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 57.9 bits (140), Expect = 4e-09
Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 9/80 (11%)
Query: 479 FKTLNRIQSRLCKSALESDENLLLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFK 538
F+ L Q ++ L +++L APTG+GKT ALL L+ + + +
Sbjct: 6 FEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRG---------KGGR 56
Query: 539 IIYVAPMRSLVQEMVGNFGK 558
++ + P R L ++ K
Sbjct: 57 VLVLVPTRELAEQWAEELKK 76
Score = 35.5 bits (82), Expect = 0.11
Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 9/52 (17%)
Query: 763 GAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPMRSLVQEMVGNFGK 814
G+GKT ALL L+ + + +++ + P R L ++ K
Sbjct: 34 GSGKTLAALLPALEALKRG---------KGGRVLVLVPTRELAEQWAEELKK 76
Score = 32.1 bits (73), Expect = 1.9
Identities = 21/70 (30%), Positives = 29/70 (41%), Gaps = 11/70 (15%)
Query: 815 DEIHLLHD-ERGPVLEALIARTIRNIEATQEDVRLVGLSATLPNYKDVATLLRIKPETGL 873
DE H L D G LE L+ +N V+L+ LSAT P + L +
Sbjct: 136 DEAHRLLDGGFGDQLEKLLKLLPKN-------VQLLLLSATPPEEIENLLELFLN---DP 185
Query: 874 FYFDNSFRPV 883
+ D F P+
Sbjct: 186 VFIDVGFTPL 195
>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
with DEXDc-, DEAD-, and DEAH-box proteins, yeast
initiation factor 4A, Ski2p, and Hepatitis C virus NS3
helicases; this domain is found in a wide variety of
helicases and helicase related proteins; may not be an
autonomously folding unit, but an integral part of the
helicase; 4 helicase superfamilies at present according
to the organization of their signature motifs; all
helicases share the ability to unwind nucleic acid
duplexes with a distinct directional polarity; they
utilize the free energy from nucleoside triphosphate
hydrolysis to fuel their translocation along DNA,
unwinding the duplex in the process.
Length = 131
Score = 54.6 bits (132), Expect = 1e-08
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 10/66 (15%)
Query: 1028 DRTLVEDLFADRHIQVLVSTATLAWGVNLPAHTVIIKGTQIYNPEKGRWVELGALDVLQM 1087
+R V F + I VLV+T +A G++LP +V+I ++P LQ
Sbjct: 66 EREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPS----------SYLQR 115
Query: 1088 LGRAGR 1093
+GRAGR
Sbjct: 116 IGRAGR 121
Score = 50.7 bits (122), Expect = 3e-07
Identities = 30/144 (20%), Positives = 55/144 (38%), Gaps = 46/144 (31%)
Query: 885 LEQQYIGVTEKKALKRFQVMNDIVYEKVMEHAGRN-QLLVFVHSRKETGKTARAIRDMCL 943
++Q + V ++K + + E + EH + ++L+F S+K
Sbjct: 2 IKQYVLPVEDEK--------LEALLELLKEHLKKGGKVLIFCPSKKML------------ 41
Query: 944 EKDTLGQFLREGSASMEVLRTEADQVKNGELRDLLPYGFAIHHAGMTRVDRTLVEDLFAD 1003
D L + LR+ + L H ++ +R V F +
Sbjct: 42 --DELAELLRKPGIKVAAL-----------------------HGDGSQEEREEVLKDFRE 76
Query: 1004 RHIQVLVSTATLAWGVNLPAHTVV 1027
I VLV+T +A G++LP +VV
Sbjct: 77 GEIVVLVATDVIARGIDLPNVSVV 100
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 56.9 bits (138), Expect = 8e-08
Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 5/89 (5%)
Query: 468 LPRYVQHAF-EDFKTLNRIQSRLCKSALESDENLLLCAPTGAGKTNVALLCMLQEIGKHI 526
L V+ F F +L Q EN+L+ APTG+GKT A L ++ E+
Sbjct: 8 LDPRVREWFKRKFTSLTPPQRYAIPEIHS-GENVLIIAPTGSGKTEAAFLPVINELLSLG 66
Query: 527 NADGTINADEFKIIYVAPMRSLVQEMVGN 555
D +Y++P+++L ++
Sbjct: 67 KGKL---EDGIYALYISPLKALNNDIRRR 92
Score = 42.6 bits (101), Expect = 0.002
Identities = 38/206 (18%), Positives = 77/206 (37%), Gaps = 44/206 (21%)
Query: 815 DEIH-LLHDERGPVLEALIARTIRNIEATQEDVRLVGLSATLPNYKDVATLLRIKPETGL 873
DEIH L +RG L + R + D + +GLSAT+ ++VA L +
Sbjct: 156 DEIHALAESKRGVQLALSLER----LRELAGDFQRIGLSATVGPPEEVAKFLVGFGDPCE 211
Query: 874 FYFDNSFRPVALEQQYIGVTEKKALKRFQVMNDIVYEKVMEHAGRNQLLVFVHSRKETGK 933
++ + + ++ + + + + + E V +H L+F ++R
Sbjct: 212 IVDVSAAKKLEIKVISPVEDLIYDEELWAALYERIAELVKKHRT---TLIFTNTRSGA-- 266
Query: 934 TARAIRDMCLEKDTLGQFLREGSASMEVLRTEADQVKNGELRDLLPYGFAIHHAGMTRVD 993
+ L L++ L P +HH ++R
Sbjct: 267 ------------ERLAFRLKK----------------------LGPDIIEVHHGSLSREL 292
Query: 994 RTLVEDLFADRHIQVLVSTATLAWGV 1019
R VE+ + ++ +V+T++L G+
Sbjct: 293 RLEVEERLKEGELKAVVATSSLELGI 318
Score = 35.7 bits (83), Expect = 0.26
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 559 DEIH-LLHDERGPVLEALIARTIRNIEATQEDVRLVGLSATLPNYKDVATLLR 610
DEIH L +RG L + R + D + +GLSAT+ ++VA L
Sbjct: 156 DEIHALAESKRGVQLALSLER----LRELAGDFQRIGLSATVGPPEEVAKFLV 204
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 48.1 bits (115), Expect = 3e-06
Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 9/61 (14%)
Query: 498 ENLLLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPMRSLVQEMVGNFG 557
++LL APTG+GKT ALL +L+ + +++ +AP R L ++
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSL---------KGGQVLVLAPTRELANQVAERLK 51
Query: 558 K 558
+
Sbjct: 52 E 52
Score = 36.2 bits (84), Expect = 0.048
Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 9/52 (17%)
Query: 763 GAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPMRSLVQEMVGNFGK 814
G+GKT ALL +L+ + +++ +AP R L ++ +
Sbjct: 10 GSGKTLAALLPILELLDSL---------KGGQVLVLAPTRELANQVAERLKE 52
>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The
Prosite family is restricted to DEAD/H helicases, whereas
this domain family is found in a wide variety of
helicases and helicase related proteins. It may be that
this is not an autonomously folding unit, but an integral
part of the helicase.
Length = 78
Score = 41.0 bits (97), Expect = 3e-04
Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 980 YGFAIHHAGMTRVDRTLVEDLFADRHIQVLVSTATLAWGVNLP-AHTVVD 1028
A H G+++ +R + + F + +VLV+T G++LP + V++
Sbjct: 8 IKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVIN 57
Score = 39.4 bits (93), Expect = 7e-04
Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 12/67 (17%)
Query: 1028 DRTLVEDLFADRHIQVLVSTATLAWGVNLP-AHTVIIKGTQIYNPEKGRWVELGALDVLQ 1086
+R + + F + +VLV+T G++LP + VI Y+ A + Q
Sbjct: 21 EREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVI-----NYDLPWNP-----ASYI-Q 69
Query: 1087 MLGRAGR 1093
+GRAGR
Sbjct: 70 RIGRAGR 76
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 42.8 bits (101), Expect = 0.002
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 7/56 (12%)
Query: 498 ENLLLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPMRSLVQEMV 553
++L APTG GKT +L+ + + + ++IYV P R+++++M
Sbjct: 215 LLVVLEAPTGYGKTEASLI-----LALALLDEKIKLKS--RVIYVLPFRTIIEDMY 263
Score = 35.9 bits (83), Expect = 0.25
Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 7/54 (12%)
Query: 756 VSFRLPRGAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPMRSLVQEMV 809
V P G GKT +L+ + + + ++IYV P R+++++M
Sbjct: 217 VVLEAPTGYGKTEASLI-----LALALLDEKIKLKS--RVIYVLPFRTIIEDMY 263
>gnl|CDD|227694 COG5407, SEC63, Preprotein translocase subunit Sec63 [Intracellular
trafficking and secretion].
Length = 610
Score = 41.9 bits (98), Expect = 0.003
Identities = 38/242 (15%), Positives = 78/242 (32%), Gaps = 47/242 (19%)
Query: 1470 LIQACVDVLSSNGWLSPAVAAMEVAQMITQAMWSKDSY-LKQLPHFNADIIKRCTEKGVE 1528
L+ A + + S+ + Q I QA+ + + QLP + + +R + + +E
Sbjct: 298 LLGALLRIASNFAFPLKECGKENKGQYIVQAIPLDHLFRILQLPRSDVEYAQRVSLRLIE 357
Query: 1529 TVFDIMELEDDDRLRLLQ-LSESQLADVARFCNRYPNI-----------ELSYEVLNKDR 1576
+ I L +L+ L +L ++ + P +L +K+R
Sbjct: 358 GMKAIGSLIAKRYGNVLKNLVVLELMEIQAVADGIPRYFLLQAPFLVFEDLFITEKSKER 417
Query: 1577 ISSGSSVNVVV------------NLDREDEVTGPVI----------------APFYPQKR 1608
+S + + N + VI AP + +
Sbjct: 418 VSLKGYLGAIPGPEHRTSALNVYNQVEISDFEASVIETGAIKNDSSDSPYSEAPDFATRN 477
Query: 1609 EEGWWVVIGDPKTNSLLSIKRLTLQQKAKIKLDF-----VAPNPGHHSYALYFMSDAYLG 1663
+ W V + + + I ++ +K+ LD VAP L + +G
Sbjct: 478 DSEWAVRVAKCEQTVYI-IPGGSIATVSKVTLDRRIQGDVAPVDKTGGKQLIVHAPFMVG 536
Query: 1664 CD 1665
Sbjct: 537 AF 538
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 39.2 bits (92), Expect = 0.020
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 12/64 (18%)
Query: 486 QSRLCKSALESDENLLLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPM 545
Q + AL +N L+ PTG GKT +A + + + K++++AP
Sbjct: 20 QLNIAAKAL--FKNTLVVLPTGLGKTFIAAMVIANRLRW----------FGGKVLFLAPT 67
Query: 546 RSLV 549
+ LV
Sbjct: 68 KPLV 71
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 38.3 bits (90), Expect = 0.041
Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 4/75 (5%)
Query: 498 ENLLLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPMRSLVQEMVGNFG 557
+N+L+ +PTG+GKT A L ++ E+ + D+ +YV+P+R+L ++ N
Sbjct: 48 KNVLISSPTGSGKTLAAFLAIIDELFRLGREGEL--EDKVYCLYVSPLRALNNDIHRNLE 105
Query: 558 K--DEIHLLHDERGP 570
+ EI + ERG
Sbjct: 106 EPLTEIREIAKERGE 120
>gnl|CDD|233483 TIGR01587, cas3_core, CRISPR-associated helicase Cas3. This model
represents the highly conserved core region of an
alignment of Cas3, a protein found in association with
CRISPR repeat elements in a broad range of bacteria and
archaea. Cas3 appears to be a helicase, with regions
found by pfam00270 (DEAD/DEAH box helicase) and
pfam00271 (Helicase conserved C-terminal domain). Some
but not all members have an N-terminal HD domain region
(pfam01966) that is not included within this model
[Mobile and extrachromosomal element functions, Other].
Length = 358
Score = 37.4 bits (87), Expect = 0.059
Identities = 23/70 (32%), Positives = 30/70 (42%), Gaps = 13/70 (18%)
Query: 500 LLLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPMRSLVQEM----VGN 555
L++ APTG GKT ALL L I K AD ++I P R+ + M
Sbjct: 2 LVIEAPTGYGKTEAALLWALHSI-KSQKAD--------RVIIALPTRATINAMYRRAKEL 52
Query: 556 FGKDEIHLLH 565
FG + L
Sbjct: 53 FGSNLGLLHS 62
>gnl|CDD|224771 COG1858, MauG, Cytochrome c peroxidase [Inorganic ion transport and
metabolism].
Length = 364
Score = 36.2 bits (84), Expect = 0.12
Identities = 24/102 (23%), Positives = 36/102 (35%), Gaps = 15/102 (14%)
Query: 379 SADARQSTSIRHQMGQGGGDGVAVVAGTRQVLDLEDLQFSSGSHFMSNKRCE-LPDG--- 434
SA S + H + +GG DG+ G ++ + F S DG
Sbjct: 75 SASGTISCATCHNLARGGVDGLPTSIGVGWA---PGPYRNAPTVFNSVFNGGQFWDGRAD 131
Query: 435 SFRKQRKGYEEVHVPALKPKPMG--PDETLVPIDKLPRYVQH 474
S +Q G P L P M P+ + ++ P YV
Sbjct: 132 SLEEQAGG------PLLNPVEMANSPERAVTKLNSDPDYVDA 167
>gnl|CDD|176111 cd08419, PBP2_CbbR_RubisCO_like, The C-terminal substrate binding of
LysR-type transcriptional regulator (CbbR) of RubisCO
operon, which is involved in the carbon dioxide fixation,
contains the type 2 periplasmic binding fold. CbbR, a
LysR-type transcriptional regulator, is required to
activate expression of RubisCO, one of two unique enzymes
in the Calvin-Benson-Bassham (CBB) cycle pathway. All
plants, cyanobacteria, and many autotrophic bacteria use
the CBB cycle to fix carbon dioxide. Thus, this cycle
plays an essential role in assimilating CO2 into organic
carbon on earth. The key CBB cycle enzyme is ribulose
1,5-bisphosphate carboxylase/oxygenase (RubisCO), which
catalyzes the actual CO2 fixation reaction. The CO2
concentration affects the expression of RubisCO genes.
It has also shown that NADPH enhances the DNA-binding
ability of the CbbR. RubisCO is composed of eight large
(CbbL) and eight small subunits (CbbS). The topology of
this substrate-binding domain is most similar to that of
the type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis.
Length = 197
Score = 35.6 bits (83), Expect = 0.12
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 1556 ARFCNRYPNIELSYEVLNKDRI 1577
FC R+P +E+S V N++++
Sbjct: 19 GAFCRRHPGVEVSLRVGNREQV 40
>gnl|CDD|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3. CRISPR
(Clustered Regularly Interspaced Short Palindromic
Repeats) and associated Cas proteins comprise a system
for heritable host defense by prokaryotic cells against
phage and other foreign DNA; DEAD/DEAH box helicase DNA
helicase cas3'; Often but not always is fused to HD
nuclease domain; signature gene for Type I.
Length = 353
Score = 36.3 bits (84), Expect = 0.14
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 9/53 (16%)
Query: 500 LLLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPMRSLVQEM 552
L++ APTG GKT ALL L + K AD ++I P R+ + M
Sbjct: 2 LVIEAPTGYGKTEAALLWALHSL-KSQKAD--------RVIIALPTRATINAM 45
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 36.4 bits (85), Expect = 0.16
Identities = 26/87 (29%), Positives = 41/87 (47%), Gaps = 20/87 (22%)
Query: 469 PRYVQHAFEDFKTL-NRI-QSRLCKSALESDENLLLCAPTGAGKTNVALLCM---LQEIG 523
Y++H T+ R+ Q L +AL+ N L+ PTG GKT +ALL + L + G
Sbjct: 1 MMYIEHPLIKPNTIEARLYQQLLAATALKK--NTLVVLPTGLGKTAIALLVIAERLHKKG 58
Query: 524 KHINADGTINADEFKIIYVAPMRSLVQ 550
K++ +AP + LV+
Sbjct: 59 G-------------KVLILAPTKPLVE 72
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 36.2 bits (84), Expect = 0.19
Identities = 11/58 (18%), Positives = 23/58 (39%), Gaps = 9/58 (15%)
Query: 493 ALESDENLLLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPMRSLVQ 550
+ N+++ TG+GKT LL +L + + + + + P +L
Sbjct: 81 LIREGRNVVVTTGTGSGKTESFLLPILDHLLR---------DPSARALLLYPTNALAN 129
Score = 31.6 bits (72), Expect = 4.6
Identities = 8/33 (24%), Positives = 18/33 (54%)
Query: 983 AIHHAGMTRVDRTLVEDLFADRHIQVLVSTATL 1015
+ + AG+ R +R +E F + + +++T L
Sbjct: 342 STYRAGLHREERRRIEAEFKEGELLGVIATNAL 374
>gnl|CDD|217503 pfam03344, Daxx, Daxx Family. The Daxx protein (also known as the
Fas-binding protein) is thought to play a role in
apoptosis, but precise role played by Daxx remains to be
determined. Daxx forms a complex with Axin.
Length = 715
Score = 35.3 bits (81), Expect = 0.37
Identities = 29/143 (20%), Positives = 61/143 (42%), Gaps = 14/143 (9%)
Query: 129 RDILCGAADEVLT--VLKNDRMKEKEKKKETENL-LGSLAEERFALLVNLGKKITDFGAE 185
R++ +EV++ +K D +E+E++K E G+ + + + A
Sbjct: 377 REVAVSRLEEVISKYAMKQDDTEEEERRKRQERERQGTSSRSSDPSKASSTSGESPSMAS 436
Query: 186 QKSTTAEENIDDTYGINVQFEESEDEDDEDTFGEVREAEELDDEGEEARVNTAIHAEN-L 244
Q+S E ++ E+E++E+ + E EE +DE EE V +E +
Sbjct: 437 QESEEEESVEEEE----------EEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEM 486
Query: 245 AGGEDAEGTGRKKDKSLHPLDID 267
G + +G G + ++ + +
Sbjct: 487 EGSSEGDGDGEEPEEDAERRNSE 509
>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit. This model
describes Pseudomonas denitrificans CobT gene product,
which is a cobalt chelatase subunit that functions in
cobalamin biosynthesis. Cobalamin (vitamin B12) can be
synthesized via several pathways, including an aerobic
pathway (found in Pseudomonas denitrificans) and an
anaerobic pathway (found in P. shermanii and Salmonella
typhimurium). These pathways differ in the point of
cobalt insertion during corrin ring formation. There are
apparently a number of variations on these two pathways,
where the major differences seem to be concerned with
the process of ring contraction. Confusion regarding the
functions of enzymes found in the aerobic vs. anaerobic
pathways has arisen because nonhomologous genes in these
different pathways were given the same gene symbols.
Thus, cobT in the aerobic pathway (P. denitrificans) is
not a homolog of cobT in the anaerobic pathway (S.
typhimurium). It should be noted that E. coli
synthesizes cobalamin only when it is supplied with the
precursor cobinamide, which is a complex intermediate.
Additionally, all E. coli cobalamin synthesis genes
(cobU, cobS and cobT) were named after their Salmonella
typhimurium homologs which function in the anaerobic
cobalamin synthesis pathway. This model describes the
aerobic cobalamin pathway Pseudomonas denitrificans CobT
gene product, which is a cobalt chelatase subunit, with
a MW ~70 kDa. The aerobic pathway cobalt chelatase is a
heterotrimeric, ATP-dependent enzyme that catalyzes
cobalt insertion during cobalamin biosynthesis. The
other two subunits are the P. denitrificans CobS
(TIGR01650) and CobN (pfam02514 CobN/Magnesium
Chelatase) proteins. To avoid potential confusion with
the nonhomologous Salmonella typhimurium/E.coli cobT
gene product, the P. denitrificans gene symbol is not
used in the name of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 600
Score = 34.9 bits (80), Expect = 0.40
Identities = 36/158 (22%), Positives = 68/158 (43%), Gaps = 23/158 (14%)
Query: 120 IQEALGDQPRDILCG-----AADEVLTVLKNDRMKEKEKKKETENLLGSLAEER-FALLV 173
+ EAL R+ L G +A ++ + +ND E + K+ + L ++ +++ FA +V
Sbjct: 133 MAEALALMVREKLTGDAPPHSAKALVDLWRND--IEAKAGKDLDRLSAAIDDQQAFARVV 190
Query: 174 -------NLGKKITDFGAEQKSTTAEENIDDTYGINVQFEESEDEDDEDTFGEVREAEEL 226
L +++ D + +S E+ DD N Q E+ E E + +E+E
Sbjct: 191 REMLRSMELAEEMGD---DTESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEAT 247
Query: 227 DDEGEEARVNTA-IHAENLA--GGEDAE--GTGRKKDK 259
D E E ++L +D+E G G + +
Sbjct: 248 DRESESGEEEMVQSDQDDLPDESDDDSETPGEGARPAR 285
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 34.9 bits (81), Expect = 0.44
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 9/58 (15%)
Query: 1036 FADRHIQVLVSTATLAWGVNLPAHTVIIKGTQIYNPEKGRWVELGALDVLQMLGRAGR 1093
F + I +LV+T + GV++P TV++ I N E+ G + Q+ GR GR
Sbjct: 529 FKEGEIDILVATTVIEVGVDVPNATVMV----IENAER-----FGLAQLHQLRGRVGR 577
>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family. All
proteins in this family for which functions are known are
3'-5' DNA-DNA helicases. These proteins are used for
recombination, recombinational repair, and possibly
maintenance of chromosome stability. 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 = 470
Score = 34.7 bits (80), Expect = 0.50
Identities = 52/248 (20%), Positives = 94/248 (37%), Gaps = 72/248 (29%)
Query: 792 EFKIIYVAPMR-----SLVQEM-----VGNFGKDEIHLL----HDERGPVLEALIARTIR 837
+ K++YV P + L+Q + + DE H + HD R P +AL
Sbjct: 101 KIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFR-PDYKAL-----G 154
Query: 838 NIEATQEDVRLVGLSATLPNY--KDVATLLRIK-PETGLFYFDNSFRPVALEQQYIGVTE 894
+++ +V ++ L+AT +D+ L +K P+ FD RP Y V
Sbjct: 155 SLKQKFPNVPIMALTATASPSVREDILRQLNLKNPQIFCTSFD---RP----NLYYEVRR 207
Query: 895 KKALKRFQVMNDIVYEKVMEHAGRNQLLVFVHSRKETGKTARAIRDMCLEKDTLGQFLRE 954
K +++ D++ E G++ + ++ SRK++ + +++
Sbjct: 208 KTP----KILEDLLRFIRKEFKGKSGI-IYCPSRKKSEQVTASLQ-------------NL 249
Query: 955 GSASMEVLRTEADQVKNGELRDLLPYGFAIHHAGMTRVDRTLVEDLFADRHIQVLVSTAT 1014
G A+ +HAG+ R V F IQV+V+T
Sbjct: 250 GIAA------------------------GAYHAGLEISARDDVHHKFQRDEIQVVVATVA 285
Query: 1015 LAWGVNLP 1022
G+N P
Sbjct: 286 FGMGINKP 293
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 34.2 bits (79), Expect = 0.71
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 9/58 (15%)
Query: 1036 FADRHIQVLVSTATLAWGVNLPAHTVIIKGTQIYNPEKGRWVELGALDVLQMLGRAGR 1093
F + + +LV+T + GV++P TV++ I + E+ G + Q+ GR GR
Sbjct: 504 FREGEVDILVATTVIEVGVDVPNATVMV----IEDAER-----FGLSQLHQLRGRVGR 552
>gnl|CDD|234127 TIGR03158, cas3_cyano, CRISPR-associated helicase Cas3, subtype
CYANO. CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) is a widespread family of
prokaryotic direct repeats with spacers of unique
sequence between consecutive repeats. This protein
family is a CRISPR-associated (Cas) family strictly
associated with the Cyano subtype of CRISPR/Cas locus,
found in several species of Cyanobacteria and several
archaeal species. It contains helicase motifs and
appears to represent the Cas3 protein of the Cyano
subtype of CRISPR/Cas system [Mobile and
extrachromosomal element functions, Other].
Length = 357
Score = 33.7 bits (77), Expect = 0.72
Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 22/77 (28%)
Query: 500 LLLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPMRSL-------VQEM 552
+ APTGAGKT L +L E I + P +L ++E
Sbjct: 17 IFNTAPTGAGKTLAWLTPLLHG--------------ENDTIALYPTNALIEDQTEAIKEF 62
Query: 553 VGNF-GKDEIHLLHDER 568
V F + +++LLH +
Sbjct: 63 VDVFKPERDVNLLHVSK 79
>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases. A diverse family of proteins
involved in ATP-dependent RNA unwinding, needed in a
variety of cellular processes including splicing,
ribosome biogenesis and RNA degradation. The name
derives from the sequence of the Walker B motif (motif
II). This domain contains the ATP- binding region.
Length = 203
Score = 33.2 bits (77), Expect = 0.74
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 10/83 (12%)
Query: 479 FKTLNRIQSRLCKSALESDENLLLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFK 538
F+ IQ+R L S +++ A TG+GKT L+ +L+ ++ + +
Sbjct: 19 FEKPTPIQARAIPPLL-SGRDVIGQAQTGSGKTAAFLIPILE----KLDPSPKKD--GPQ 71
Query: 539 IIYVAPMRSL---VQEMVGNFGK 558
+ +AP R L + E+ GK
Sbjct: 72 ALILAPTRELALQIAEVARKLGK 94
>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA
ligase-associated. Members of this protein family are
DEAD/DEAH box helicases found associated with a
bacterial ATP-dependent DNA ligase, part of a four-gene
system that occurs in about 12 % of prokaryotic
reference genomes. The actual motif in this family is
DE[VILW]H.
Length = 803
Score = 34.1 bits (79), Expect = 0.81
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 5/56 (8%)
Query: 493 ALESDENLLLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPMRSL 548
A + LL APTG+GKT L L ++ A +Y+ P+R+L
Sbjct: 24 AALEGRSGLLIAPTGSGKTLAGFLPSLIDL-----AGPEKPKKGLHTLYITPLRAL 74
Score = 32.5 bits (75), Expect = 2.6
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 983 AIHHAGMTRVDRTLVEDLFADRHIQVLVSTATLAWGVNLPAHTVVDR 1029
A+HH + R R VE A ++ +V T++L GV+ VD
Sbjct: 279 ALHHGSLDREQRRWVEAAMAAGRLRAVVCTSSLDLGVDFGP---VDL 322
Score = 31.7 bits (73), Expect = 3.7
Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 559 DEIH-LLHDERGPVLEALIARTIRNIEATQEDVRLVGLSATLPN 601
DE H L +RG LE +AR + +R GLSAT+ N
Sbjct: 147 DEWHELAGSKRGDQLELALAR----LRRLAPGLRRWGLSATIGN 186
Score = 31.7 bits (73), Expect = 3.7
Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 815 DEIH-LLHDERGPVLEALIARTIRNIEATQEDVRLVGLSATLPN 857
DE H L +RG LE +AR + +R GLSAT+ N
Sbjct: 147 DEWHELAGSKRGDQLELALAR----LRRLAPGLRRWGLSATIGN 186
>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor
[Transcription].
Length = 392
Score = 33.9 bits (77), Expect = 0.85
Identities = 28/123 (22%), Positives = 48/123 (39%), Gaps = 11/123 (8%)
Query: 143 LKNDRMKEKEKKKETENLLGSLAEERFALLVNLGKKITDFGAEQKSTTAEENIDDTYGIN 202
L +K++++ E E G E+ + K G +++ EN +
Sbjct: 252 LSRPALKKEKQGAEEEGEEGMSEEDLDVGAAEIENKEVSEGDKEQQQEEVENAEAHKE-- 309
Query: 203 VQFEESEDEDDEDTFGEVREAEELDDEGEEARVNTAIHAENLAGGEDA-EGTGRKKDKSL 261
E D DE E +E DDE EE +T + A+ L E E R+ + +
Sbjct: 310 ---EVQSDRPDEIG-----EEKEEDDENEENERHTELLADELNELEKGIEEKRRQMESAT 361
Query: 262 HPL 264
+P+
Sbjct: 362 NPI 364
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 31.4 bits (72), Expect = 0.92
Identities = 24/107 (22%), Positives = 41/107 (38%), Gaps = 24/107 (22%)
Query: 493 ALESDENLLLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPMRSLV-QE 551
L + L+ TG+GKT A + + + + K+++V P + L+ Q
Sbjct: 14 RLLEKKRGLIVMATGSGKTLTAAALIAR-----------LAKGKKKVLFVVPRKDLLEQA 62
Query: 552 MVGNFGKDEIHLLHDERGPVLEALIARTIRNIEATQEDVRLVGLSAT 598
+V DE H + R I + L+GL+AT
Sbjct: 63 LV--IIIDEAHHSSAKTK----------YRKILEKFKPAFLLGLTAT 97
>gnl|CDD|218115 pfam04502, DUF572, Family of unknown function (DUF572). Family of
eukaryotic proteins with undetermined function.
Length = 321
Score = 33.2 bits (76), Expect = 1.1
Identities = 15/73 (20%), Positives = 28/73 (38%), Gaps = 5/73 (6%)
Query: 316 DCFDFIKMLKKYRQMILYCTLLASSQSESERQKLRDTMSEDPALAKILRQLDTG-KNEDG 374
D ML+ + + E E + L ++S P + R+ D +D
Sbjct: 165 ADVDVNSMLEALFRREKK----EEEEEEEEDEALIKSLSFGPETEEDRRRADDEDSEDDE 220
Query: 375 DANDSADARQSTS 387
+ ND+ + +S S
Sbjct: 221 EDNDNTPSPKSGS 233
>gnl|CDD|227297 COG4962, CpaF, Flp pilus assembly protein, ATPase CpaF
[Intracellular trafficking and secretion].
Length = 355
Score = 33.1 bits (76), Expect = 1.2
Identities = 25/95 (26%), Positives = 39/95 (41%), Gaps = 15/95 (15%)
Query: 430 ELPDGSFRKQRKGYEEVHVPALKPKPMGPDETLVPIDKLPRYVQ--HAFEDFKTLNRIQS 487
LPDGS + A P P+ D + I K P+ F T+ R +
Sbjct: 116 RLPDGS-----------RLNANSP-PVAIDGPTLSIRKFPKIKLTLLDLIIFGTMIRRAA 163
Query: 488 RLCKSALESDENLLLCAPTGAGKTNVALLCMLQEI 522
+ + A+ N+L+ TG+GKT + L + I
Sbjct: 164 KFLRRAVGIRCNILISGGTGSGKTTL-LNALSGFI 197
>gnl|CDD|222875 PHA02558, uvsW, UvsW helicase; Provisional.
Length = 501
Score = 33.1 bits (76), Expect = 1.6
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 10/56 (17%)
Query: 501 LLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPMRSLVQEMVGNF 556
LL PT AGK+ + +L + + E K++ + P SLV +M+ +F
Sbjct: 133 LLNLPTSAGKS--LIQYLL--------SRYYLENYEGKVLIIVPTTSLVTQMIDDF 178
>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain
fusion protein; Provisional.
Length = 131
Score = 31.5 bits (71), Expect = 1.7
Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 10/71 (14%)
Query: 183 GAEQKSTTAEENIDDTYGINVQFEESEDEDDEDTFGEVREAEELDDEGEEARVNTAIHAE 242
G +T A E ++ E ++ ++D D E EA+ D+ EE + A+
Sbjct: 61 GPAAAATAAAEAAEEA-------EAADADEDAD---EAAEADAADEADEEEETDEAVDET 110
Query: 243 NLAGGEDAEGT 253
+AE
Sbjct: 111 ADEADAEAEEA 121
>gnl|CDD|182531 PRK10538, PRK10538, malonic semialdehyde reductase; Provisional.
Length = 248
Score = 32.4 bits (74), Expect = 1.7
Identities = 26/80 (32%), Positives = 44/80 (55%), Gaps = 11/80 (13%)
Query: 950 QFLREGSASMEVLRTEADQVKNGELRDLLPYGFAIHHAGMTRVDRTLVEDLFAD-----R 1004
+F+++G +V+ T Q + EL+D L G ++ A + +R +E++ A R
Sbjct: 19 RFIQQGH---KVIATGRRQERLQELKDEL--GDNLYIAQLDVRNRAAIEEMLASLPAEWR 73
Query: 1005 HIQVLVSTATLAWGVNLPAH 1024
+I VLV+ A LA G+ PAH
Sbjct: 74 NIDVLVNNAGLALGLE-PAH 92
>gnl|CDD|225410 COG2854, Ttg2D, ABC-type transport system involved in resistance to
organic solvents, auxiliary component [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 202
Score = 32.0 bits (73), Expect = 1.9
Identities = 23/92 (25%), Positives = 40/92 (43%), Gaps = 7/92 (7%)
Query: 116 LLSFIQEALGDQPRDILCGAADEVLTVLKNDRMKEK--EKKKET--ENLLGSLAEERFAL 171
S + A P ++ AAD+VL++LKN++ K K + + L + ++A
Sbjct: 17 FASSLAAAAPANPYSLVQEAADKVLSILKNNQAKIKQDPQYLRQIVDQELLPYVDFKYAA 76
Query: 172 LVNLGKKITDFGAEQKS---TTAEENIDDTYG 200
+ LGK EQ+ ++ TYG
Sbjct: 77 KLVLGKYYKTASPEQRQAFFKAFRTYLEQTYG 108
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 33.0 bits (75), Expect = 2.0
Identities = 23/131 (17%), Positives = 48/131 (36%), Gaps = 7/131 (5%)
Query: 130 DILCGAADEVLTVLKNDRMKEKEKKKETENLLGS-LAEERFALLVNLGKKITDFGAEQKS 188
D+ ++ + D + E E N L + ++ F+ L +K+ + G E+
Sbjct: 4012 DMEAADENKEEADAEKDEPMQDEDPLEENNTLDEDIQQDDFSDLAEDDEKMNEDGFEENV 4071
Query: 189 TTAEENIDDTYGINVQFEESEDEDDEDTFGEVR-EAEELDDEGEEARVNTAIHAENLAGG 247
EE+ +D + + E+ E +D+ + +A+ E NT
Sbjct: 4072 QENEESTEDGVKSDEELEQGEVPEDQAIDNHPKMDAKSTFASAEADEENTDKGI-----V 4126
Query: 248 EDAEGTGRKKD 258
+ E G +
Sbjct: 4127 GENEELGEEDG 4137
>gnl|CDD|227563 COG5238, RNA1, Ran GTPase-activating protein (RanGAP) involved in
mRNA processing and transport [Signal transduction
mechanisms / RNA processing and modification].
Length = 388
Score = 32.6 bits (74), Expect = 2.1
Identities = 22/82 (26%), Positives = 29/82 (35%)
Query: 167 ERFALLVNLGKKITDFGAEQKSTTAEENIDDTYGINVQFEESEDEDDEDTFGEVREAEEL 226
N K++ DFG + + + +V EES DE+ ED E
Sbjct: 306 VDLERNGNRIKELADFGDYYEDIFEVVEVVEKQEGDVVTEESTDEESEDEVEIDESVIEE 365
Query: 227 DDEGEEARVNTAIHAENLAGGE 248
E E V AE LA E
Sbjct: 366 VAEMELLEVQVDDLAERLAETE 387
>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT
(nicotinate-mononucleotide:5, 6-dimethylbenzimidazole
phosphoribosyltransferase) [Coenzyme metabolism].
Length = 620
Score = 32.5 bits (74), Expect = 2.6
Identities = 36/147 (24%), Positives = 67/147 (45%), Gaps = 16/147 (10%)
Query: 120 IQEALGDQPRDILCG-----AADEVLTVLKNDRMKEKEKKKETENLLGSLAEER-FALLV 173
++EA+ R+ L G +A +VL + +++ E + ++ + L + +++ FA +V
Sbjct: 152 LEEAVALLVREKLTGDAPPDSAGKVLDLWRDE--IEDKAGEDLDGLAAEIDDQQAFARVV 209
Query: 174 -------NLGKKITDFGAEQKSTTAEENIDDTYGINVQFEESEDEDDEDTFGEVREAEEL 226
++ ++ D G E+ E+ DD N E +E + E EAE
Sbjct: 210 RDMLGSMDMAEETGDDGIEE-DADEEDGDDDQPDNNEDSEAGREESEGSDESEEDEAEAT 268
Query: 227 DDEGEEARVNTAIHAENLAGGEDAEGT 253
D EGEE ++ A +E+ E E T
Sbjct: 269 DGEGEEGEMDAAEASEDSESDESDEDT 295
>gnl|CDD|178706 PLN03161, PLN03161, Probable xyloglucan
endotransglucosylase/hydrolase protein; Provisional.
Length = 291
Score = 31.8 bits (72), Expect = 2.9
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 1471 IQACVDVLSSNGWLSPAVAAMEVAQMITQAMWSKDSYL-----KQLPHFNADIIKRCTEK 1525
I+ C D SN W SP+ + + AQ+ TQ +D+++ K FN + C +
Sbjct: 231 IKQCADPTPSNWWTSPSYSQLTNAQL-TQMKKVRDNFMIYDYCKDTKRFNGVMPPECFKP 289
>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 = 31.0 bits (70), Expect = 3.2
Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 2/70 (2%)
Query: 184 AEQKSTTAEENIDDTYGINVQFEESEDEDDEDTFGEVREAEELDDEGEEARVNTAIHAEN 243
T EE D+ V+ +E E ED ED+ E E EE ++ EE ++ + +
Sbjct: 12 VRPPPTKDEEEDWDSQAEEVEEDEEEMEDWEDSLDE--EDEEAEEVEEETAASSKAPSSS 69
Query: 244 LAGGEDAEGT 253
+
Sbjct: 70 SKSSSQETIS 79
>gnl|CDD|233660 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB. This model
represents HrpB, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria,
but also in a few species of other lineages. The member
from Rhizobium meliloti has been designated HelO. HrpB
is typically about 800 residues in length, while its
paralog HrpA (TIGR01967), also uncharacterized, is about
1300 amino acids long. Related characterized eukarotic
proteins are RNA helicases associated with pre-mRNA
processing [Unknown function, Enzymes of unknown
specificity].
Length = 819
Score = 32.1 bits (73), Expect = 3.5
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 491 KSALESDENLLLCAPTGAGKTNVALLCMLQEIGKH 525
+ AL + ++L AP GAGK+ L +L G
Sbjct: 11 RDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGIG 45
>gnl|CDD|211788 TIGR03098, ligase_PEP_1, acyl-CoA ligase (AMP-forming), exosortase
A-associated. This group of proteins contains an
AMP-binding domain (pfam00501) associated with acyl
CoA-ligases. These proteins are generally found in
genomes containing the exosortase/PEP-CTERM protein
expoert system , specifically the type 1 variant of this
system described by the Genome Property GenProp0652. When
found in this context they are invariably present next to
a decarboxylase enzyme. A number of sequences from
Burkholderia species also hit this model, but the genomic
context is obviously different. The hypothesis of a
constant substrate for this family is only strong where
the exosortase context is present.
Length = 517
Score = 31.7 bits (72), Expect = 3.7
Identities = 28/122 (22%), Positives = 54/122 (44%), Gaps = 15/122 (12%)
Query: 983 AIHHAGMTRVDRTLVEDLFADRHIQVLVS--TATLAWGVNLPAHTVVDRTLVEDLFADRH 1040
+ G+ R +R + + D+ ++ + + A LA GV +P + ++ V + AD +
Sbjct: 41 GLRGLGLARGERVAI---YLDKRLETVTAMFGAALAGGVFVPINPLLKAEQVAHILADCN 97
Query: 1041 IQVLVSTA--------TLAWGVNLPAHTVIIKGTQIYNPEKGRWVELGALDVLQMLGRAG 1092
+++LV+++ L +L T+II G + E E + L LG A
Sbjct: 98 VRLLVTSSERLDLLHPALPGCHDL--RTLIIVGDPAHASEGHPGEEPASWPKLLALGDAD 155
Query: 1093 RP 1094
P
Sbjct: 156 PP 157
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 31.9 bits (73), Expect = 3.8
Identities = 19/119 (15%), Positives = 48/119 (40%), Gaps = 2/119 (1%)
Query: 135 AADEVLTVLKNDRMKEKEKKKETENLLGSLAEERFALLVNLGKKITDFGAE--QKSTTAE 192
+ T K K KKK + L S E+ L + ++ +
Sbjct: 75 PKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQADDDD 134
Query: 193 ENIDDTYGINVQFEESEDEDDEDTFGEVREAEELDDEGEEARVNTAIHAENLAGGEDAE 251
++ DD + ++ +D++D+D + + ++ D+E +EA+ + ++ ++ +
Sbjct: 135 DDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDD 193
>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family.
Prothymosin alpha and parathymosin are two ubiquitous
small acidic nuclear proteins that are thought to be
involved in cell cycle progression, proliferation, and
cell differentiation.
Length = 106
Score = 29.9 bits (67), Expect = 3.8
Identities = 16/45 (35%), Positives = 21/45 (46%)
Query: 189 TTAEENIDDTYGINVQFEESEDEDDEDTFGEVREAEELDDEGEEA 233
EEN ++ EE DEDDE+ GE E E ++E E
Sbjct: 37 NENEENGAQEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEEEETEG 81
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 31.6 bits (72), Expect = 3.9
Identities = 13/40 (32%), Positives = 22/40 (55%)
Query: 983 AIHHAGMTRVDRTLVEDLFADRHIQVLVSTATLAWGVNLP 1022
A +HAG+ R V++ F +Q++V+T G+N P
Sbjct: 264 AAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKP 303
>gnl|CDD|218538 pfam05285, SDA1, SDA1. This family consists of several SDA1
protein homologues. SDA1 is a Saccharomyces cerevisiae
protein which is involved in the control of the actin
cytoskeleton. The protein is essential for cell
viability and is localised in the nucleus.
Length = 317
Score = 31.5 bits (72), Expect = 4.0
Identities = 21/56 (37%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 204 QFEESEDEDDEDTFGEVREAEELDDEGEEARVNTAIHAENLAGGEDAEGTGRKKDK 259
Q ES+D+DDE+ EV E E+ DDEGE V + + ED E K
Sbjct: 90 QGLESDDDDDEEEEWEVEEDEDSDDEGEWIDVESDKE-IESSDSEDEEEKDEAAKK 144
>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein. This protein is found to be part
of a large ribonucleoprotein complex containing the U3
snoRNA. Depletion of the Utp proteins impedes production
of the 18S rRNA, indicating that they are part of the
active pre-rRNA processing complex. This large RNP
complex has been termed the small subunit (SSU)
processome.
Length = 728
Score = 31.6 bits (72), Expect = 4.2
Identities = 26/143 (18%), Positives = 50/143 (34%), Gaps = 19/143 (13%)
Query: 142 VLKNDRMKEKEKKKETEN------LLGSLAEERFALLVNLGKKITDFGAEQKSTTAEENI 195
+L M+ E +K+ EN L L E + E+ +++N+
Sbjct: 373 LLSMKFMQRAEARKKEENDAEIEELRRELEGEE------------ESDEEENEEPSKKNV 420
Query: 196 D-DTYGINVQFEESEDEDDEDTFGEVREAEELDDEGEEARVNTAIHAENLAGGEDAEGTG 254
+G +E+E + + + ++ DE EE E +A
Sbjct: 421 GRRKFGPENGEKEAESKKLKKENKNEFKEKKESDEEEELEDEEEAKVEKVANKLLKRSEK 480
Query: 255 RKKDKSLHPLDIDAYWLQRRLSK 277
+K++ LD + WL+ S
Sbjct: 481 AQKEEEEEELDEENPWLKTTSSV 503
>gnl|CDD|234502 TIGR04212, GlyGly_RbtA, Acinetobacter rhombotarget A. Members of
this protein family are found, so far, exclusively in
the genus Acinetobacter. Members average just over 600
amino acids in length, including a 22-amino acid
C-terminal putative protein sorting recognition
sequence, GlyGly-CTERM (TIGR03501). The GlyGly-CTERM
signal always co-occurs with a subfamily of the rhomboid
family intramembrane serine proteases called
rhombosortase (TIGR03902). Members occur paired with a
second rhombosortase target, with which it also shares
an N-terminal motif CSLREA. This protein is designated
Acinetobacter rhombotarget A (rbtA).
Length = 605
Score = 31.7 bits (72), Expect = 4.3
Identities = 27/109 (24%), Positives = 47/109 (43%), Gaps = 10/109 (9%)
Query: 199 YGINVQFEESEDEDDEDTFGEVREAEELDDEGEEARVNTAIHAENLAGGEDAEGT---GR 255
Y ++Q + DED +DT +REA E ++ + + GG+DA T R
Sbjct: 18 YSADIQVTTTVDEDKDDTVCSLREAVEYINQRMPDQYEAGYNG---CGGKDASSTIILER 74
Query: 256 KKDKSLHP-LDIDAYWLQRRLSKIYDDAMVSQAKAGEVLNILKSAGDDR 303
K+ L+ ++I A + YD ++ + G +K G D+
Sbjct: 75 DKEYKLNNHIEIKA---DLTIRTAYDTSVFETDQPGLNNATIKMVGSDQ 120
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 31.5 bits (72), Expect = 4.3
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 983 AIHHAGMTRVDRTLVEDLFADRHIQVLVSTATLAWGVNLP 1022
+HAG++ +R V+ F + I+V+V+T G++ P
Sbjct: 258 GAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKP 297
>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein.
Length = 306
Score = 31.0 bits (70), Expect = 5.5
Identities = 14/55 (25%), Positives = 21/55 (38%)
Query: 183 GAEQKSTTAEENIDDTYGINVQFEESEDEDDEDTFGEVREAEELDDEGEEARVNT 237
G + E DD YG F E ++ E E E EE+++ E+
Sbjct: 41 GDDAIELAEPETSDDPYGNPDPFGEDDEGRIEVRISEDGEEEEVEEGEEDEEEEG 95
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 31.3 bits (72), Expect = 6.3
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 4/37 (10%)
Query: 1036 FADRHIQVLVSTATLAWGVNLPAHTVIIKGTQIYNPE 1072
F I +LV+T + GV++P TV++ I N E
Sbjct: 527 FKAGEIDILVATTVIEVGVDVPNATVMV----IENAE 559
>gnl|CDD|187841 cd09710, Cas3_I-D, CRISPR/Cas system-associated protein Cas3;
Distinct diverged subfamily of Cas3 helicase domain.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Diverged DNA helicase Cas3'; signature gene for Type I
and subtype I-D.
Length = 353
Score = 31.0 bits (70), Expect = 6.4
Identities = 18/77 (23%), Positives = 28/77 (36%), Gaps = 22/77 (28%)
Query: 500 LLLCAPTGAGKTNVALLCMLQEIGKHINADGTINADEFKIIYVAPMRSL-------VQEM 552
+ APTGAGKT L +L E K I + P +L ++E
Sbjct: 17 IFNTAPTGAGKTLAWLTPLLHG--------------ENKAIALYPTNALIEDQTEAIKEF 62
Query: 553 VGNF-GKDEIHLLHDER 568
V + + ++ L
Sbjct: 63 VDDANPRHQVKSLSASD 79
>gnl|CDD|187536 cd05193, AR_like_SDR_e, aldehyde reductase, flavonoid reductase, and
related proteins, extended (e) SDRs. This subgroup
contains aldehyde reductase and flavonoid reductase of
the extended SDR-type and related proteins. Proteins in
this subgroup have a complete SDR-type active site tetrad
and a close match to the canonical extended SDR
NADP-binding motif. Aldehyde reductase I (aka carbonyl
reductase) is an NADP-binding SDR; it catalyzes the
NADP-dependent reduction of ethyl
4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. The related flavonoid
reductases act in the NADP-dependent reduction of
flavonoids, ketone-containing plant secondary
metabolites. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates, lipids,
aromatic compounds, and amino acids, and act in redox
sensing. Classical SDRs have an TGXXX[AG]XG cofactor
binding motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and Lys,
there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate binding
is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a 4-pro-S
hydride transfer and proton relay involving the conserved
Tyr and Lys, a water molecule stabilized by Asn, and
nicotinamide. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different from
the forms normally seen in classical or extended SDRs.
Complex (multidomain) SDRs such as ketoreductase domains
of fatty acid synthase have a GGXGXXG NAD(P)-binding
motif and an altered active site motif (YXXXN). Fungal
type ketoacyl reductases have a TGXXXGX(1-2)G
NAD(P)-binding motif.
Length = 295
Score = 30.7 bits (69), Expect = 6.5
Identities = 17/56 (30%), Positives = 22/56 (39%), Gaps = 4/56 (7%)
Query: 1193 HTAALHLERSGLIKY--DRKSGHMQVTELGRIASHYYCTHETMATYNQLLKPTLSE 1246
+ AL L G + D H+ EL Y CT +N LLK TL +
Sbjct: 213 VSPALALIPPGYYVHVVDICLAHIGCLELPIARGRYICTAGNF-DWNTLLK-TLRK 266
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 29.6 bits (66), Expect = 7.3
Identities = 17/136 (12%), Positives = 42/136 (30%), Gaps = 22/136 (16%)
Query: 498 ENLLLCAPTGAGKTNVALLCMLQEIGKH-----INADGTINADEFKIIYVAPMRSLVQEM 552
E +L+ P G+GKT +A + I+ + + +++ +
Sbjct: 3 EVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGS 62
Query: 553 VGNFGK----------------DEIHLLHDERGPVLEALIART-IRNIEATQEDVRLVGL 595
+ DEI L D L L+ + + +++++ ++
Sbjct: 63 GELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILT 122
Query: 596 SATLPNYKDVATLLRI 611
+ + R
Sbjct: 123 TNDEKDLGPALLRRRF 138
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 29.8 bits (67), Expect = 7.6
Identities = 26/118 (22%), Positives = 39/118 (33%), Gaps = 21/118 (17%)
Query: 494 LESDENLLLCAPTGAGKTNVALLCMLQEIGKHINADGT----INADEFKIIYVAPMRSLV 549
L +NLLL P G GKT +A + I + G +NA + V
Sbjct: 16 LPPPKNLLLYGPPGTGKTTLA-----RAIANELFRPGAPFLYLNASDLLEGLVVAELFGH 70
Query: 550 QEMVGNFGK-----------DEIHLLHDERGPVLEALIARTIRNIEATQEDVRLVGLS 596
+ F DEI L L ++ E+VR++G +
Sbjct: 71 FLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDR-ENVRVIGAT 127
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This protein
contains an ATP/GTP binding P-loop motif. It is found
associated with IS21 family insertion sequences. The
function of this protein is unknown, but it may perform
a transposase function.
Length = 178
Score = 29.9 bits (68), Expect = 8.2
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 494 LESDENLLLCAPTGAGKTNVA 514
+E ENLLL P G GKT++A
Sbjct: 44 IEQAENLLLLGPPGVGKTHLA 64
>gnl|CDD|235027 PRK02301, PRK02301, putative deoxyhypusine synthase; Provisional.
Length = 316
Score = 30.4 bits (69), Expect = 8.5
Identities = 19/42 (45%), Positives = 23/42 (54%), Gaps = 10/42 (23%)
Query: 987 AGMTRVDRTLVEDLFADRHIQVLVSTATLAWGVNLPAHTVVD 1028
AGM R +V DL D HI VLV+T G NL H V++
Sbjct: 71 AGM----RGIVSDLIRDGHIDVLVTT-----GANL-THDVIE 102
>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein. The proteins in this family
are designated YL1. These proteins have been shown to be
DNA-binding and may be a transcription factor.
Length = 238
Score = 30.0 bits (68), Expect = 9.1
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 6/48 (12%)
Query: 191 AEENIDDTYGINVQFEESEDEDDEDTFGEVREAEELD-----DEGEEA 233
E D+ + + FEE E++D+E E E EE+D E +E
Sbjct: 20 EELEEDEFFWTYLLFEE-EEDDEEFEIEEEEEEEEVDSDFDDSEDDEP 66
>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM). This
family consists of several Plasmodium falciparum SPAM
(secreted polymorphic antigen associated with
merozoites) proteins. Variation among SPAM alleles is
the result of deletions and amino acid substitutions in
non-repetitive sequences within and flanking the alanine
heptad-repeat domain. Heptad repeats in which the a and
d position contain hydrophobic residues generate
amphipathic alpha-helices which give rise to helical
bundles or coiled-coil structures in proteins. SPAM is
an example of a P. falciparum antigen in which a
repetitive sequence has features characteristic of a
well-defined structural element.
Length = 164
Score = 29.4 bits (66), Expect = 9.2
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 20/83 (24%)
Query: 149 KEKEKKKETENLLGSLAEERFALLVNLGKKITDFGAEQKSTTAEENIDDTYGINVQFEES 208
K+ E++K+ ENLL + KIT + E E+ D+ +E
Sbjct: 11 KKPEEEKKDENLLEHV-------------KITSWDKEDIIKENEDVKDEK-------QED 50
Query: 209 EDEDDEDTFGEVREAEELDDEGE 231
++E++E+ E+ E E+++DE E
Sbjct: 51 DEEEEEEDEEEIEEPEDIEDEEE 73
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 30.5 bits (69), Expect = 9.3
Identities = 17/55 (30%), Positives = 24/55 (43%)
Query: 185 EQKSTTAEENIDDTYGINVQFEESEDEDDEDTFGEVREAEELDDEGEEARVNTAI 239
EQ +T A E D+ V D DD++ E + +E DDE E+ I
Sbjct: 3 EQVNTQANEEEDEEELEAVARSAGSDSDDDEVPAEDEDEDEEDDEEAESPAKAEI 57
>gnl|CDD|233148 TIGR00844, c_cpa1, na(+)/h(+) antiporter. The Monovalent
Cation:Proton Antiporter-1 (CPA1) Family (TC 2.A.36) The
CPA1 family is a large family of proteins derived from
Gram-positive and Gram-negative bacteria, blue green
bacteria, yeast, plants and animals. Transporters from
eukaryotes have been functionally characterized, and all
of these catalyze Na+:H+ exchange. Their primary
physiological functions may be in (1) cytoplasmic pH
regulation, extruding the H+ generated during
metabolism, and (2) salt tolerance (in plants), due to
Na+ uptake into vacuoles. This model is specific for the
fungal members of this family [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 810
Score = 30.7 bits (69), Expect = 9.3
Identities = 34/173 (19%), Positives = 64/173 (36%), Gaps = 21/173 (12%)
Query: 137 DEVLTVLKNDRMKEKEKKKETENLLGSLAEERFALLVNLGKKITDF-GAEQKSTTAEENI 195
E+ + + KEKE T +L + LG + G E++S T +
Sbjct: 526 IEMNDLGRERLQKEKEAHAATFDLSTTTTT-------QLGTENGRGGGLEERSKTNIKER 578
Query: 196 DDTYGINVQFEESEDEDDEDTFGEVREAEELDDEGEEARVNT-AIHAENLAGGEDAEGTG 254
+ ++ + + V + E E V T +E++A E
Sbjct: 579 SENVNTIYGLDKLARDTENRDVTYVPTSRYDGIESEIDDVYTYENDSESIASSE------ 632
Query: 255 RKKDKSLHPLDIDAYWLQRRLSKIYDDAMVSQAKAGEVLNILKSAGDD-RDAE 306
R++ K L + AY ++ D+ ++ + + GE+L + RDAE
Sbjct: 633 RRRIKKLREEEQQAY-----IAYTEDNQVIIENRQGEILEYVDIHDRGARDAE 680
>gnl|CDD|165116 PHA02749, PHA02749, hypothetical protein; Provisional.
Length = 322
Score = 30.3 bits (68), Expect = 9.5
Identities = 31/164 (18%), Positives = 60/164 (36%), Gaps = 29/164 (17%)
Query: 1006 IQVLVSTATLAWGVNLPAHTVVDRTLVEDLFADRHI------------QVLVSTATLAWG 1053
I++ LA ++ A T+VD V F R I L + + A G
Sbjct: 75 IKLAADGHILAAWIDTIASTIVDAIFVT-AFTRRDIIGSDLIRKGLVVFFLFAWSIAALG 133
Query: 1054 VNLPA-HTVIIKGTQI-YNPEKGRWVELGAL---DVLQMLGRAGRPQYDTKGEGVLITNH 1108
+N+ A H I G + G ++ + L ++ + R + +++ +
Sbjct: 134 LNILAWHPEISAGFHFPLHLIAGAFIAIAGLLLPIIIVLTYRGEAGGIPPGRDILMLLFN 193
Query: 1109 -----------SELQYYLSLLNHQLPVESQMISKLPDMLNAEIV 1141
S+ + + QL + S ++ LPD + A I+
Sbjct: 194 AFAMLIASYFLSDALAQIHIAEQQLGITSTFLASLPDFITAFII 237
>gnl|CDD|132382 TIGR03339, phn_lysR, aminoethylphosphonate catabolism associated LysR
family transcriptional regulator. This group of
sequences represents a number of related clades with
numerous examples of members adjacent to operons for the
degradation of 2-aminoethylphosphonate (AEP) in
Pseudomonas, Ralstonia, Bordetella and Burkholderia
species. These are transcriptional regulators of the LysR
family which contain a helix-turn-helix (HTH) domain
(pfam00126) and a periplasmic substrate-binding
protein-like domain (pfam03466).
Length = 279
Score = 30.1 bits (68), Expect = 9.7
Identities = 31/98 (31%), Positives = 39/98 (39%), Gaps = 24/98 (24%)
Query: 1527 VETVFDIMELEDDDRLR-LLQLSESQL---AD--------VARFCNRYPNIELSYEVLNK 1574
VE +F E E + LR L E L A VARF RYP IE+S + N
Sbjct: 64 VERLFQ-QEAEAEFLLRESGALREGSLRIAATAPYYVLDLVARFRQRYPGIEVSVRIGNS 122
Query: 1575 D---------RISSGSSVNVVVN--LDREDEVTGPVIA 1601
R+ S VV + LDR P++A
Sbjct: 123 QEVLQALQSYRVDVAVSSEVVDDPRLDRVVLGNDPLVA 160
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
0.319 0.136 0.390
Gapped
Lambda K H
0.267 0.0705 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 87,562,640
Number of extensions: 9032205
Number of successful extensions: 9248
Number of sequences better than 10.0: 1
Number of HSP's gapped: 9024
Number of HSP's successfully gapped: 171
Length of query: 1689
Length of database: 10,937,602
Length adjustment: 110
Effective length of query: 1579
Effective length of database: 6,058,662
Effective search space: 9566627298
Effective search space used: 9566627298
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 66 (29.2 bits)