RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7952
(444 letters)
>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch
repair, nucleotide-binding, DNA-binding, polymorphism,
nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens}
PDB: 2wwy_A*
Length = 591
Score = 320 bits (821), Expect = e-104
Identities = 92/301 (30%), Positives = 146/301 (48%), Gaps = 27/301 (8%)
Query: 144 SGQTKTENKAILEELRLVKPRIKLLYVTPERAVTE-SFHYLLQHLVRYNKLAYIVVDEAH 202
+ +K K + E+ +KL+YVTPE+ F L+ + I VDE H
Sbjct: 116 ASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVDEVH 175
Query: 203 CVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTS 262
C S+WGHDFRP Y+ LG L++ N +I LTATA V D +L K F S
Sbjct: 176 CCSQWGHDFRPDYKALGILKRQFPN-ASLIGLTATATNHVLTDAQKILCIEKC-FTFTAS 233
Query: 263 TFRSNLFYDVIF-DDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALR 321
R NL+Y+V +D + + I GIIYC +++ + + +L+
Sbjct: 234 FNRPNLYYEVRQKPSNTEDFIEDIVKLI-----NGRYKGQSGIIYCFSQKDSEQVTVSLQ 288
Query: 322 RK----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSI 371
+ +++ V + EI V+ AT++FGMGID+ +VRFV+H M S+
Sbjct: 289 NLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSM 348
Query: 372 PAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYC 431
YYQESGRAGRD +++ C +Y+ + ++ + + +++L M+ YC
Sbjct: 349 ENYYQESGRAGRDDMKADCILYYGFGDIFRISSMVVME-NVGQQKLY-------EMVSYC 400
Query: 432 E 432
+
Sbjct: 401 Q 401
Score = 47.3 bits (113), Expect = 8e-06
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 3/68 (4%)
Query: 10 SSAVGKSSSLTGNQQDRKGGKVS-EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDI 68
S G S+ + ++ L+ +F + F+ LQ + I + ++
Sbjct: 5 DSDAGASNEYDSSPAAWNKEDFPWSGKVKDILQNVFKLEKFR-PLQLETINVTMAG-KEV 62
Query: 69 FVSMPTGA 76
F+ MPTG
Sbjct: 63 FLVMPTGG 70
>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix,
helix-turn-helix, ATP binding, Zn(2+) binding,
hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43
c.37.1.19 c.37.1.19 PDB: 1oyy_A*
Length = 523
Score = 305 bits (783), Expect = 4e-99
Identities = 98/299 (32%), Positives = 161/299 (53%), Gaps = 29/299 (9%)
Query: 144 SGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHC 203
S QT+ + ++ R +I+LLY+ PER + ++F L H + VDEAHC
Sbjct: 97 STQTREQQLEVMTGCR--TGQIRLLYIAPERLMLDNFLEHLAHW----NPVLLAVDEAHC 150
Query: 204 VSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTST 263
+S+WGHDFRP Y LG+LRQ +P +ALTATA+ + +QDI+ +L N P + +S
Sbjct: 151 ISQWGHDFRPEYAALGQLRQRFPT-LPFMALTATADDTTRQDIVRLLGLNDP-LIQISSF 208
Query: 264 FRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK 323
R N+ Y ++ + ++++ + GIIYC +R D A L+ K
Sbjct: 209 DRPNIRYMLMEKF---KPLDQLMRYVQE------QRGKSGIIYCNSRAKVEDTAARLQSK 259
Query: 324 ----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPA 373
+ + R+ VQE F R ++ ++ AT++FGMGI++ NVRFVVH+ +P +I +
Sbjct: 260 GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIES 319
Query: 374 YYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCE 432
YYQE+GRAGRDGL + +++ L + + + + +++ +M + E
Sbjct: 320 YYQETGRAGRDGLPAEAMLFYDPADMAWLRRCL--EEKPQGQLQDIERHKLNAMGAFAE 376
Score = 45.6 bits (109), Expect = 2e-05
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGA 76
E L+ FG+ F+ Q++ I +L D V MPTG
Sbjct: 10 ESGAKQVLQETFGYQQFR-PGQEEIIDTVLSG-RDCLVVMPTGG 51
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 65.5 bits (159), Expect = 2e-11
Identities = 74/490 (15%), Positives = 137/490 (27%), Gaps = 188/490 (38%)
Query: 32 SEQELTAKLKALF-GFDSFKCE-LQKKAIRHIL-----------LRTHDI------FVSM 72
+ EL K F G+ S E + +L L +DI +
Sbjct: 56 TPAELVGK----FLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQE 111
Query: 73 PTGAVSLVGSVV----SARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTS 128
+ ++ +AR + P +S R +
Sbjct: 112 NDTTLVKTKELIKNYITARIMAKRP-----------------FDKKSNSALFR------A 148
Query: 129 IVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHY---LLQ 185
+ G + L I GQ T++ EELR LY T V + + L
Sbjct: 149 VGEGNAQLV---AIFGGQGNTDD--YFEELRD-------LYQTYHVLVGDLIKFSAETLS 196
Query: 186 HLVR----YNKLAYIVVDEAHCVSEWGH--DFRPTYRRLGELRQFTGN---SIPIIALTA 236
L+R K+ ++ + EW P + + + S P+I +
Sbjct: 197 ELIRTTLDAEKVFTQGLN----ILEWLENPSNTPD-------KDYLLSIPISCPLIGVIQ 245
Query: 237 TA-----------EPS-----------VKQDIISVLKFNKPYKVFKTS-TFRSNLFYDVI 273
A P Q +++ + + ++ S F+
Sbjct: 246 LAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAV-------AIAETDSWES--FFV-S 295
Query: 274 FDDLLK----------DSYAHVKEFIEKCLGKDNKANNCGI----IYCR--TREHTTDLA 317
+ ++Y + + + +D+ NN G+ + T+E D
Sbjct: 296 VRKAITVLFFIGVRCYEAYPNT--SLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYV 353
Query: 318 DALRRKVNKH--ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYY 375
+ K N H +V EI+++ +N VV G P S+
Sbjct: 354 N----KTNSHLPAGKQV-------EISLVNG---------AKN--LVVS-GPPQSLYGLN 390
Query: 376 Q--ESGRAGRDGLQSYCRI-------------------YHSEHSKKSLEYVIKTDTSTKR 414
+A QS RI +HS + + +I D
Sbjct: 391 LTLRKAKAPSGLDQS--RIPFSERKLKFSNRFLPVASPFHSHLLVPASD-LINKDLVKNN 447
Query: 415 EQL---ELKF 421
+++
Sbjct: 448 VSFNAKDIQI 457
Score = 46.6 bits (110), Expect = 2e-05
Identities = 52/318 (16%), Positives = 93/318 (29%), Gaps = 127/318 (39%)
Query: 17 SSLTGNQQDRKGGKVSEQELTAKLKALFG-FDSFKCELQKKAIR---HILLRTHDIFVSM 72
TG+ Q + +TA A ++SF +KAI I +R ++ +
Sbjct: 268 KGATGHSQG-----L----VTAVAIAETDSWESFF-VSVRKAITVLFFIGVRCYEAY--- 314
Query: 73 PTGAVSLVGSVVSARSRVRIPPG--ADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV 130
+PP D + N G SP+LS
Sbjct: 315 ---------------PNTSLPPSILEDSLENNE-----GVPSPMLS-------------- 340
Query: 131 TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYV----TPERAV----TESFHY 182
+S T+ + + + + P K + + + V +S
Sbjct: 341 ------------ISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQS--- 385
Query: 183 LLQHLVRYNKLAYIVVDEAHCVSEWGHD-----FRPTYRRLGELRQFTGNSIPIIA---- 233
L L + +A S G D F R+L +F +P+ +
Sbjct: 386 -LYGLNLT-------LRKAKAPS--GLDQSRIPFSE--RKLKFSNRF----LPVASPFHS 429
Query: 234 -LTATAEPSVKQDIISV-LKFNK-----PYKVFKTST---FRS-------NLFYDVIF-- 274
L A + +D++ + FN P V+ T R + D I
Sbjct: 430 HLLVPASDLINKDLVKNNVSFNAKDIQIP--VYDTFDGSDLRVLSGSISERIV-DCIIRL 486
Query: 275 ----DDLLKDSYAHVKEF 288
+ + H+ +F
Sbjct: 487 PVKWETTTQFKATHILDF 504
Score = 42.7 bits (100), Expect = 3e-04
Identities = 77/450 (17%), Positives = 124/450 (27%), Gaps = 187/450 (41%)
Query: 6 SKDASSAVGKSSSLTGNQQDRKGGKVSEQELTAKLKALFG--------FDSFKCELQK-- 55
K ++SA+ ++ GN A+L A+FG F+ EL+
Sbjct: 138 DKKSNSALFRAVG-EGN---------------AQLVAIFGGQGNTDDYFE----ELRDLY 177
Query: 56 ---KAIRHILLRTHDI----FVSMPTGAVSLVGSVVSARSRVRIP---PGADFILNGNVR 105
+ L++ + A + ++ + P P D++L+
Sbjct: 178 QTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLS---- 233
Query: 106 SRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQL-----ELIVSGQTKTENKAILEELRL 160
PI S L I + QL + G T E ++ L+
Sbjct: 234 ------IPI--SCPL--------IG-----VIQLAHYVVTAKLLGFTPGELRSYLKGATG 272
Query: 161 VKPRIKLLYVTPERAVT-------ESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRP 213
+ VT AV ESF ++ + L +I V + +
Sbjct: 273 HSQGL----VT---AVAIAETDSWESFFVSVRKAITV--LFFIGV-RCYEA------YPN 316
Query: 214 TYRRLGELRQFT--GNSIP----------------IIALTATAEPSVKQDIISVLKFNKP 255
T L +P + T + P+ KQ IS+ N
Sbjct: 317 TSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISL--VNGA 374
Query: 256 ------------Y-------KVFKTST-------FR------SNLFYDVIF----DDLLK 279
Y K S F SN F + LL
Sbjct: 375 KNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRF-LPVASPFHSHLLV 433
Query: 280 DSYAHVKEFIEKCLGKDN---KANNCGI-IYCRTREHTTDLADALRRKVNKHERSRVQES 335
+ I K L K+N A + I +Y T D +D
Sbjct: 434 P----ASDLINKDLVKNNVSFNAKDIQIPVY-----DTFDGSD----------------- 467
Query: 336 FMRGEINVITATISFGMGIDRQNVRFVVHW 365
+R I+ I +D +R V W
Sbjct: 468 -LRVLSGSISERI-----VD-CIIRLPVKW 490
>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer,
ATP-binding, helicase, hydrolase, nucleotide-binding;
2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A
Length = 212
Score = 58.5 bits (142), Expect = 3e-10
Identities = 35/120 (29%), Positives = 54/120 (45%), Gaps = 15/120 (12%)
Query: 303 GIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGM 352
+++ RT+ T ++A L R +++ ER RV +F +GE+ V+ AT
Sbjct: 34 AMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAAR 93
Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQESG---RAGRDGLQSYCRIYHSEHSK-KSLEYVIKT 408
G+D V VVH+ +P AY SG RAGR G E ++LE +
Sbjct: 94 GLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGR-VVLLYGPRERRDVEALERAVGR 152
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 58.2 bits (141), Expect = 2e-09
Identities = 51/328 (15%), Positives = 103/328 (31%), Gaps = 65/328 (19%)
Query: 142 IVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL--VRYNKLAYIVVD 199
S K E + + I L + + + ++ + + ++ VD
Sbjct: 97 FYSSMKKEEKEKFEKSFEEDDYHI--LVFSTQF--------VSKNREKLSQKRFDFVFVD 146
Query: 200 EAHCVSEWGHD------FRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFN 253
+ D L + I A + + + +
Sbjct: 147 DV--------DAVLKASRNI--DTLLMMVGIPEEII-RKAFSTIKQGKIYERP---KNLK 192
Query: 254 KPYKVFKTSTFRSNLFYDVIFDDLL--------------KDSYAHVKEFIEKCLGKDNKA 299
V ++T + ++F DLL + EK +
Sbjct: 193 PGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRISSRSK-EKLVELLEIF 251
Query: 300 NNCGIIYCRTREHTTDLADALRRK-----VNKHERSRVQESFMRGEINVITATISFGM-- 352
+ +I+ +T E +L + L+R E + E F G+IN++ ++
Sbjct: 252 RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEFEKNFEDFKVGKINILIGVQAYYGKL 311
Query: 353 --GID-RQNVRFVVHWGMPSSIPA--YYQESGRAGRDGLQSYCRIY-----HSEHSKKSL 402
G+D + +++V+ WG PS Y Q SGR+ R + E +SL
Sbjct: 312 TRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFESL 371
Query: 403 EYVIKTDT-STKREQLELKFKNYLSMLE 429
+ + E+ E +K + +E
Sbjct: 372 KTRLLLIAEEEIIEEAEANWKELVHEVE 399
>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein,
ATPase, RNA binding protein; 3.00A {Methanocaldococcus
jannaschii} SCOP: c.37.1.19 c.37.1.19
Length = 367
Score = 56.0 bits (136), Expect = 8e-09
Identities = 32/131 (24%), Positives = 64/131 (48%), Gaps = 19/131 (14%)
Query: 303 GIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGM 352
G+++C+T+ T +LA LR +++ +R +V F + +I ++ AT
Sbjct: 241 GLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSR 300
Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQESG---RAGRDGLQSYCRIYHSEHSK-KSLEYVIKT 408
GID ++ V+++ +P + +Y G RAG+ G + I E+ K + +E +K
Sbjct: 301 GIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGK-AISIINRREYKKLRYIERAMK- 358
Query: 409 DTSTKREQLEL 419
K ++L+
Sbjct: 359 ---LKIKKLKF 366
>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA
recognition motif, ATP-BIND helicase,
nucleotide-binding; 2.80A {Thermus thermophilus}
Length = 300
Score = 55.1 bits (133), Expect = 1e-08
Identities = 36/120 (30%), Positives = 54/120 (45%), Gaps = 15/120 (12%)
Query: 303 GIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGM 352
+++ RT+ T ++A L R +++ ER RV +F +GE+ V+ AT
Sbjct: 31 AMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAAR 90
Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQESG---RAGRDGLQSYCRIYHSEHSK-KSLEYVIKT 408
G+D V VVH+ MP AY SG RAGR G E ++LE +
Sbjct: 91 GLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGR-VVLLYGPRERRDVEALERAVGR 149
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 56.0 bits (134), Expect = 2e-08
Identities = 54/350 (15%), Positives = 108/350 (30%), Gaps = 96/350 (27%)
Query: 27 KG-GK---VSEQELTAKLKALFGFDSF-----KCELQKKAIRHILLRTHDI---FVSMPT 74
G GK + L+ K++ F F C + + + + I + S
Sbjct: 159 LGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSD 218
Query: 75 GAVSLVGSVVSARSRVRI----PPGAD--FILNGNVRSRNGWISPILSSFYL-------- 120
+ ++ + S ++ +R P + +L NV + ++F L
Sbjct: 219 HSSNIKLRIHSIQAELRRLLKSKPYENCLLVLL-NV-----QNAKAWNAFNLSCKILLTT 272
Query: 121 RFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVT--- 177
RF+ + + L+ T E K++L L+ + R + L P +T
Sbjct: 273 RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL--LKYLDCRPQDL---PREVLTTNP 327
Query: 178 -------ESFHYLLQHLVRYNKLAYIVVDEAHCVSEWG------HDFRPTYRRLGELRQF 224
ES L ++ ++ D+ + E ++R + RL
Sbjct: 328 RRLSIIAESIR---DGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFP-- 382
Query: 225 TGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAH 284
S I P + +++DVI D++
Sbjct: 383 --PSAHI-----------------------PTILLSL------IWFDVIKSDVMVV---- 407
Query: 285 VKEFIEKCL-GKDNKANNCGI--IYCRTREHTTDLADALRRKVNKHERSR 331
V + + L K K + I IY + + R V+ + +
Sbjct: 408 VNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPK 457
Score = 44.1 bits (103), Expect = 1e-04
Identities = 31/209 (14%), Positives = 67/209 (32%), Gaps = 44/209 (21%)
Query: 90 VRIPPGADFILNGNVRSRNGWISPILSSFY---LRFRDDKTSIVTGRSDLYQLELIVSGQ 146
IP ++ +V + + +++ + L + K S ++ + + L + +
Sbjct: 385 AHIPTILLSLIWFDVIKSD--VMVVVNKLHKYSLVEKQPKESTIS----IPSIYLELKVK 438
Query: 147 TKTE---NKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHC 203
+ E +++I++ + K + P + ++ HL +
Sbjct: 439 LENEYALHRSIVDHYNIPK-TFDSDDLIPPYLDQYFYSHIGHHLKNIEH-----PERMTL 492
Query: 204 VSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTST 263
DFR F I TA + + LKF KPY
Sbjct: 493 FRMVFLDFR-----------FLEQKI-RHDSTAWNASGSILNTLQQLKFYKPY------- 533
Query: 264 FRSNLFYDVIFDDLLKDSYAHVKEFIEKC 292
N D ++ L+ + +F+ K
Sbjct: 534 ICDN---DPKYERLVNA----ILDFLPKI 555
Score = 43.3 bits (101), Expect = 1e-04
Identities = 38/251 (15%), Positives = 72/251 (28%), Gaps = 73/251 (29%)
Query: 244 QDIISVL--KFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAH----------------- 284
+DI+SV F + ++ D ++ A
Sbjct: 19 KDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEM 78
Query: 285 VKEFIEKCLGKDNK--------------ANNCGIIYCRTREHTTDLADALRRKVNKHERS 330
V++F+E+ L + K I R R + + + K+ S
Sbjct: 79 VQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDN------QVFAKYNVS 132
Query: 331 RVQESF--------MRGEINVITATISFGM-GIDRQ----NV--RFVVHWGMPSSIPAYY 375
R+Q +R NV+ G+ G + +V + V M I ++
Sbjct: 133 RLQPYLKLRQALLELRPAKNVLI----DGVLGSGKTWVALDVCLSYKVQCKMDFKI--FW 186
Query: 376 QESGRAGRDG-----LQSYC-RIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLE 429
LQ +I + S+ IK ++ + + L
Sbjct: 187 LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI----HSIQAELRRLLKSKP 242
Query: 430 YCEQGYFLVIL 440
Y L++L
Sbjct: 243 YENC---LLVL 250
>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase;
RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo
sapiens} SCOP: c.37.1.19
Length = 172
Score = 53.0 bits (128), Expect = 2e-08
Identities = 22/92 (23%), Positives = 38/92 (41%), Gaps = 10/92 (10%)
Query: 304 IIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMG 353
+I+ ++ + LA L + + + ER + F + ++ AT FG G
Sbjct: 35 VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG 94
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
+D + V ++ MP Y RAGR G
Sbjct: 95 MDIERVNIAFNYDMPEDSDTYLHRVARAGRFG 126
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
termination, binding, hydrolase, membrane, mRNA
transport; 2.80A {Schizosaccharomyces pombe}
Length = 508
Score = 54.9 bits (133), Expect = 3e-08
Identities = 23/102 (22%), Positives = 39/102 (38%), Gaps = 19/102 (18%)
Query: 304 IIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMG 353
II+C+ ++ ++A + + +R + +SF G V+ T G
Sbjct: 361 IIFCKKKDTAEEIARRMTADGHTVACLTGNLEGAQRDAIMDSFRVGTSKVLVTTNVIARG 420
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQE---------SGRAGRDGL 386
ID V VV++ MP +GR GR G+
Sbjct: 421 IDVSQVNLVVNYDMPLDQAGRPDPQTYLHRIGRTGRFGRVGV 462
>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene
regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19
c.37.1.19 PDB: 1xtj_A* 1xtk_A
Length = 391
Score = 53.7 bits (130), Expect = 5e-08
Identities = 22/92 (23%), Positives = 37/92 (40%), Gaps = 10/92 (10%)
Query: 304 IIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISFGMG 353
+I+ ++ + LA L + + ER + F + ++ AT FG G
Sbjct: 254 VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG 313
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
+D + V ++ MP Y RAGR G
Sbjct: 314 MDIERVNIAFNYDMPEDSDTYLHRVARAGRFG 345
>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein,
translation; 2.50A {Saccharomyces cerevisiae} SCOP:
c.37.1.19 PDB: 2vso_A* 2vsx_A*
Length = 394
Score = 52.9 bits (128), Expect = 9e-08
Identities = 25/96 (26%), Positives = 42/96 (43%), Gaps = 13/96 (13%)
Query: 304 IIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISFGMG 353
+I+C TR +L LR + + ER + + F G ++ +T G
Sbjct: 263 VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG 322
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQ---ESGRAGRDGL 386
ID Q V V+++ +P++ Y GR GR G+
Sbjct: 323 IDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGV 358
>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural
genomics, structural consortium, SGC, alternative
initiation, ATP-binding, devel protein; 2.80A {Homo
sapiens}
Length = 175
Score = 50.7 bits (122), Expect = 1e-07
Identities = 23/102 (22%), Positives = 41/102 (40%), Gaps = 19/102 (18%)
Query: 304 IIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMG 353
II+C+TR + L + + + +R+ + + F G+ V+ T G
Sbjct: 38 IIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARG 97
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQE---------SGRAGRDGL 386
ID + V VV++ +P +GR G+ GL
Sbjct: 98 IDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGL 139
>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis,
cell cycle, nucleus, phosph RNA-binding, ATP-binding,
helicase, hydrolase; 3.50A {Homo sapiens}
Length = 414
Score = 52.6 bits (127), Expect = 1e-07
Identities = 23/96 (23%), Positives = 39/96 (40%), Gaps = 13/96 (13%)
Query: 304 IIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISFGMG 353
+I+ TR L + + +++ ER + F G V+ T G
Sbjct: 284 VIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARG 343
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQ---ESGRAGRDGL 386
ID Q V V+++ +P++ Y GR GR G+
Sbjct: 344 IDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGV 379
>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation,
rRNA processing, mRNA splicing, mRNA transport; HET:
ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB:
2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B
2zu6_A
Length = 410
Score = 52.2 bits (126), Expect = 2e-07
Identities = 22/97 (22%), Positives = 43/97 (44%), Gaps = 13/97 (13%)
Query: 303 GIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGM 352
+I+C T+ L + +R + + ER + + F G V+ +T +
Sbjct: 279 AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWAR 338
Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQ---ESGRAGRDGL 386
G+D V ++++ +P++ Y SGR GR G+
Sbjct: 339 GLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGV 375
>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein,
translation; 1.75A {Saccharomyces cerevisiae} SCOP:
c.37.1.19
Length = 165
Score = 49.9 bits (120), Expect = 2e-07
Identities = 25/92 (27%), Positives = 41/92 (44%), Gaps = 10/92 (10%)
Query: 304 IIYCRTREHTTDLADALR----------RKVNKHERSRVQESFMRGEINVITATISFGMG 353
+I+C TR +L LR + + ER + + F G ++ +T G
Sbjct: 34 VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG 93
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
ID Q V V+++ +P++ Y GR GR G
Sbjct: 94 IDVQQVSLVINYDLPANKENYIHRIGRGGRFG 125
>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding,
RNA binding protein; 2.10A {Saccharomyces cerevisiae}
SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A
Length = 400
Score = 51.0 bits (123), Expect = 4e-07
Identities = 24/97 (24%), Positives = 41/97 (42%), Gaps = 15/97 (15%)
Query: 304 IIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISFGMG 353
II+C + LA + ++ + ER++V F +G++ + + G
Sbjct: 262 IIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRG 321
Query: 354 IDRQNVRFVVHWGMPSSIPAYY----QESGRAGRDGL 386
ID Q V V+++ P + Y SGR G GL
Sbjct: 322 IDIQAVNVVINFDFPKT-AETYLHRIGRSGRFGHLGL 357
>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA
dependent ATPase, mRNA export, nucleocytoplasmic
transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens}
PDB: 3ews_A* 3g0h_A* 3fhc_B
Length = 412
Score = 50.2 bits (121), Expect = 6e-07
Identities = 25/102 (24%), Positives = 43/102 (42%), Gaps = 19/102 (18%)
Query: 304 IIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMG 353
+I+C TR+ + LA L ++ + +R+ V E F G+ V+ T G
Sbjct: 270 MIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARG 329
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQE---------SGRAGRDGL 386
ID + V V+++ +P +GR G+ GL
Sbjct: 330 IDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGL 371
>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore
complex, nucleocytoplasmic trans mRNA export, protein
interaction, beta-propeller; HET: ADP; 3.19A {Homo
sapiens}
Length = 479
Score = 50.0 bits (120), Expect = 1e-06
Identities = 25/102 (24%), Positives = 43/102 (42%), Gaps = 19/102 (18%)
Query: 304 IIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMG 353
+I+C TR+ + LA L ++ + +R+ V E F G+ V+ T G
Sbjct: 337 MIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARG 396
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQE---------SGRAGRDGL 386
ID + V V+++ +P +GR G+ GL
Sbjct: 397 IDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGL 438
>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA
repair, DNA recombina hydrolase; 2.90A {Pyrococcus
furiosus} SCOP: c.37.1.19 c.37.1.19
Length = 494
Score = 49.8 bits (118), Expect = 1e-06
Identities = 28/118 (23%), Positives = 46/118 (38%), Gaps = 20/118 (16%)
Query: 284 HVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------------------VN 325
+KE I + L + + I++ RE + + L + ++
Sbjct: 347 KLKEIIREQLQRKQNSK--IIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLS 404
Query: 326 KHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGR 383
+ E+ + + F RGE NV+ AT G+D V VV + S Q GR GR
Sbjct: 405 QREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGR 462
Score = 28.2 bits (62), Expect = 6.2
Identities = 26/175 (14%), Positives = 60/175 (34%), Gaps = 15/175 (8%)
Query: 166 KLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFT 225
K++ TP+ + LL + ++ IV DEAH Y + +
Sbjct: 103 KVIVATPQTIE----NDLLAGRISLEDVSLIVFDEAHRAVG-----NYAYVFIAREYKRQ 153
Query: 226 GNSIPIIALTATAEPSVK--QDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDL---LKD 280
+ +I LTA+ + + ++I+ L + S + F+ + L +
Sbjct: 154 AKNPLVIGLTASPGSTPEKIMEVINNLGIEHIEYRSENSPDVRPYVKGIRFEWVRVDLPE 213
Query: 281 SYAHVKEFIEKCLGKD-NKANNCGIIYCRTREHTTDLADALRRKVNKHERSRVQE 334
Y V++ + + L G++ + + + +N+ +
Sbjct: 214 IYKEVRKLLREMLRDALKPLAETGLLESSSPDIPKKEVLRAGQIINEEMAKGNHD 268
>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase;
1.95A {Bacillus subtilis}
Length = 163
Score = 46.7 bits (112), Expect = 2e-06
Identities = 30/97 (30%), Positives = 43/97 (44%), Gaps = 15/97 (15%)
Query: 303 GIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGM 352
II+CRT+EH L D L + + +R V F RGE + AT
Sbjct: 38 CIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAAR 97
Query: 353 GIDRQNVRFVVHWGMPSSIPAYY----QESGRAGRDG 385
GID +N+ V+++ +P Y +GRAG G
Sbjct: 98 GIDIENISLVINYDLPLE-KESYVHRTGRTGRAGNKG 133
>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase,
mRNA-export, nuclear pore, hydrolase-RNA complex; HET:
ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A*
3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A
3pev_A* 3peu_A*
Length = 395
Score = 48.3 bits (116), Expect = 3e-06
Identities = 24/102 (23%), Positives = 39/102 (38%), Gaps = 19/102 (18%)
Query: 304 IIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMG 353
II+ T++ L L+ + + ER R+ + F G V+ T G
Sbjct: 247 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 306
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQE---------SGRAGRDGL 386
ID V VV++ +P+ +GR GR G+
Sbjct: 307 IDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGV 348
>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics,
structural genomic consortium, SGC, hydrolase; 2.60A
{Homo sapiens}
Length = 191
Score = 46.5 bits (111), Expect = 4e-06
Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 10/92 (10%)
Query: 304 IIYCRTREHTTDLADALRRK----VNKH------ERSRVQESFMRGEINVITATISFGMG 353
+I+ + + + L K V H ER++ E+F G+ +V+ AT G
Sbjct: 58 LIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKG 117
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
+D ++ V+++ MP I Y GR G G
Sbjct: 118 LDFPAIQHVINYDMPEEIENYVHRIGRTGCSG 149
>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA
helicase, DEAD-BOX, ATP-binding, HE hydrolase,
mitochondrion; HET: ANP; 1.90A {Saccharomyces
cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A*
Length = 563
Score = 47.5 bits (113), Expect = 5e-06
Identities = 55/265 (20%), Positives = 101/265 (38%), Gaps = 55/265 (20%)
Query: 156 EELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR-----YNKLAYIVVDEAHCVSEWGHD 210
++ K R ++ TP R L+ L + + + Y V+DEA D
Sbjct: 193 AMNKMNKLRPNIVIATPGR--------LIDVLEKYSNKFFRFVDYKVLDEA--------D 236
Query: 211 ------FRPTYRR----LGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVF- 259
FR L E + ++I + +AT + V++ ++ NK +F
Sbjct: 237 RLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQK--LANNIMNKKECLFL 294
Query: 260 ------KTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHT 313
+ + V+ + +S E I+K + K+ +N II+ T + T
Sbjct: 295 DTVDKNEPEA-HERIDQSVVISEKFANSIFAAVEHIKKQI-KERDSNYKAIIFAPTVKFT 352
Query: 314 TDLADALRRKVNK-------------HERSRVQESFMRGEINVITATISFGMGIDRQNVR 360
+ L L+ + K ++R+ + + F + E ++ T G+D NV
Sbjct: 353 SFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVH 412
Query: 361 FVVHWGMPSSIPAYYQESGRAGRDG 385
V+ G+PS + Y GR R G
Sbjct: 413 EVLQIGVPSELANYIHRIGRTARSG 437
>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA
dependent ATPase, RNA helicase; HET: ANP; 1.91A
{Saccharomyces cerevisiae S288C}
Length = 579
Score = 46.7 bits (111), Expect = 1e-05
Identities = 56/262 (21%), Positives = 101/262 (38%), Gaps = 55/262 (20%)
Query: 159 RLVKPRIKLLYVTPERAVTESFHYLLQHLVR-----YNKLAYIVVDEAHCVSEWGHD--- 210
++ K R ++ TP R L+ L + + + Y V+DEA D
Sbjct: 145 KMNKLRPNIVIATPGR--------LIDVLEKYSNKFFRFVDYKVLDEA--------DRLL 188
Query: 211 ---FRPTYRR----LGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVF---- 259
FR L E + ++I + +AT + V++ ++ NK +F
Sbjct: 189 EIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQK--LANNIMNKKECLFLDTV 246
Query: 260 ---KTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDL 316
+ + V+ + +S E I+K + K+ +N II+ T + T+ L
Sbjct: 247 DKNEPEA-HERIDQSVVISEKFANSIFAAVEHIKKQI-KERDSNYKAIIFAPTVKFTSFL 304
Query: 317 ADALRRKVNK-------H------ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVV 363
L+ + K H +R+ + + F + E ++ T G+D NV V+
Sbjct: 305 CSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVL 364
Query: 364 HWGMPSSIPAYYQESGRAGRDG 385
G+PS + Y GR R G
Sbjct: 365 QIGVPSELANYIHRIGRTARSG 386
>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation,
nucleotide-binding, hydrolase, RNA-binding, ATP-binding,
DNA-binding, nuclear protein; 1.91A {Homo sapiens}
Length = 185
Score = 43.3 bits (103), Expect = 3e-05
Identities = 27/110 (24%), Positives = 47/110 (42%), Gaps = 11/110 (10%)
Query: 286 KEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----VNKH------ERSRVQES 335
+ F+ L K + +++ T++ L D L + + H +R
Sbjct: 33 RSFLLDLLNATGKDSLT-LVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQ 91
Query: 336 FMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
F G+ ++ AT G+D NV+ V+++ +PS I Y GR GR G
Sbjct: 92 FRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVG 141
>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity
A; hydrolase inhibitor-hydrolase complex, DEAD box RNA
helicase; 2.90A {Escherichia coli}
Length = 170
Score = 42.6 bits (101), Expect = 5e-05
Identities = 28/96 (29%), Positives = 43/96 (44%), Gaps = 13/96 (13%)
Query: 304 IIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMG 353
I++ R RE +LA+ LR + + +R+ + G +NV+ AT G
Sbjct: 34 IVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARG 93
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQE---SGRAGRDGL 386
ID +V V ++ MP S Y + RAGR G
Sbjct: 94 IDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGT 129
>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription
factor, RNA polymerase recycling, activator,
ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}
Length = 968
Score = 44.7 bits (105), Expect = 6e-05
Identities = 22/128 (17%), Positives = 43/128 (33%), Gaps = 14/128 (10%)
Query: 304 IIYCRTREHTTDLADALRRK-----------VNKHERSRVQESFMRGE--INVITATISF 350
++ C L LR + ++ ER R F + V+ +
Sbjct: 507 LVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIG 566
Query: 351 GMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDT 410
G + Q +V + +P + Q GR R G +I+ + +K+ + V+
Sbjct: 567 SEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHV-PYLEKTAQSVLVRWY 625
Query: 411 STKREQLE 418
+ E
Sbjct: 626 HEGLDAFE 633
Score = 38.5 bits (89), Expect = 0.004
Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 8/64 (12%)
Query: 179 SFHYLLQHLVRYNKLA-----YIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIA 233
S + + R L +VVDEAH + Y+ + Q + ++
Sbjct: 255 SLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQA---IEQLAEHVPGVLL 311
Query: 234 LTAT 237
LTAT
Sbjct: 312 LTAT 315
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding,
hydrolase, nucleotide- binding; 2.00A {Pyrococcus
furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*
Length = 720
Score = 44.5 bits (105), Expect = 6e-05
Identities = 31/133 (23%), Positives = 50/133 (37%), Gaps = 22/133 (16%)
Query: 315 DLADALRRKVNKH-------ERSRVQESFMRGEINVITATISFGMGID--------RQNV 359
LA A+R V H ER V+E+F +G I + AT + GI+ R
Sbjct: 288 KLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIW 347
Query: 360 RFVVHWGMPSSIPAYYQESGRAGRDGLQSYCR---IYHSEHSKKSLEYVIKTDTSTKREQ 416
R+ I +Q GRAGR + S+ ++ + + I E+
Sbjct: 348 RYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPREVMNHYIFGKP----EK 403
Query: 417 LELKFKNYLSMLE 429
L + N ++
Sbjct: 404 LFSQLSNESNLRS 416
>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD;
ATP-binding, hydrolase, nucleotide-binding, RNA binding
protein, structural genomics; 1.90A {Sulfolobus
tokodaii}
Length = 337
Score = 43.6 bits (104), Expect = 7e-05
Identities = 22/93 (23%), Positives = 36/93 (38%), Gaps = 11/93 (11%)
Query: 303 GIIYCRTREHTTDLADALRRKVNKH------ERSRVQESFMRGEINVITATISFGMGIDR 356
I++ RTR L + R+R ++F GE +++ T G+D
Sbjct: 223 VIVFVRTRNRVAKLVRLFDNAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDI 282
Query: 357 QNVRFVVHWGMPSSIPAYY----QESGRAGRDG 385
V V+++ P Y +GR GR G
Sbjct: 283 PLVEKVINFDAP-QDLRTYIHRIGRTGRMGRKG 314
>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin
nucleotide-binding; 2.30A {Sulfolobus solfataricus}
Length = 715
Score = 42.0 bits (99), Expect = 3e-04
Identities = 30/135 (22%), Positives = 49/135 (36%), Gaps = 20/135 (14%)
Query: 315 DLADALRRKVNKH-------ERSRVQESFMRGEINVITATISFGMGI------------D 355
L + + V H R ++E F + +I VI AT + G+
Sbjct: 306 LLKSLISKGVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIY 365
Query: 356 RQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKRE 415
R N + ++ I Y Q SGRAGR G K+ ++ V K + E
Sbjct: 366 RFNKKIAGYY-DEIPIMEYKQMSGRAGRPGFDQIGESIVVVRDKEDVDRVFKKYVLSDVE 424
Query: 416 QLELKFKNYLSMLEY 430
+E K + + +
Sbjct: 425 PIESKLGSERAFYTF 439
Score = 31.2 bits (71), Expect = 0.74
Identities = 9/49 (18%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 30 KVSEQELTAKLKALFGFDSFKC--ELQKKAIRHILLRTHDIFVSMPTGA 76
+ + +L + + + K Q +A++ LL + + ++ PTG+
Sbjct: 9 PIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGS 57
>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC,
structural GE consortium, hydrolase; HET: AMP; 2.20A
{Homo sapiens}
Length = 417
Score = 41.8 bits (99), Expect = 4e-04
Identities = 27/110 (24%), Positives = 47/110 (42%), Gaps = 11/110 (10%)
Query: 286 KEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----VNKH------ERSRVQES 335
+ F+ L K + +++ T++ L D L + + H +R
Sbjct: 263 RSFLLDLLNATGKDSLT-LVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQ 321
Query: 336 FMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
F G+ ++ AT G+D NV+ V+++ +PS I Y GR GR G
Sbjct: 322 FRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVG 371
>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal
helicase, DNA repair,, DNA binding protein/DNA complex;
3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2
c.37.1.19 c.37.1.19 PDB: 2p6u_A
Length = 702
Score = 41.3 bits (97), Expect = 6e-04
Identities = 29/132 (21%), Positives = 51/132 (38%), Gaps = 21/132 (15%)
Query: 315 DLADALRRKVNKH-------ERSRVQESFMRGEINVITATISFGMGIDRQNV--RFVV-- 363
LA+ +R+ H +R V+++F RG I V+ AT + G+ N+ R V+
Sbjct: 290 KLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGV---NLPARRVIVR 346
Query: 364 ------HWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQL 417
+ + Y Q +GRAGR G+ + E +K + E++
Sbjct: 347 SLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRD-REIAVKRYIFGEPERI 405
Query: 418 ELKFKNYLSMLE 429
K +
Sbjct: 406 TSKLGVETHLRF 417
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 39.2 bits (90), Expect = 7e-04
Identities = 8/25 (32%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 216 RRL-GELRQFTGNSIPIIALTATAE 239
++L L+ + +S P +A+ AT E
Sbjct: 23 KKLQASLKLYADDSAPALAIKATME 47
>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex,
ATPase, riken structural genomics/proteomics initiative,
RSGI; HET: ANP; 2.20A {Drosophila melanogaster}
Length = 434
Score = 39.5 bits (93), Expect = 0.002
Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 10/92 (10%)
Query: 304 IIYCRTREHTTDLADALRRK----VNKH------ERSRVQESFMRGEINVITATISFGMG 353
I++ T+ LA L K + H +R + F G + V+ AT G
Sbjct: 304 IVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRG 363
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
+D +N++ V+++ MPS I Y GR GR G
Sbjct: 364 LDIKNIKHVINYDMPSKIDDYVHRIGRTGRVG 395
>3h1t_A Type I site-specific restriction-modification system, R
(restriction) subunit; hydrolase, restriction enzyme
HSDR, ATP-binding; 2.30A {Vibrio vulnificus}
Length = 590
Score = 38.2 bits (89), Expect = 0.005
Identities = 29/181 (16%), Positives = 53/181 (29%), Gaps = 46/181 (25%)
Query: 195 YIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVL---- 250
I++DE H S +R + L F I +TAT +D
Sbjct: 305 LIIIDECHRGS---ARDNSNWREI--LEYF--EPAFQIGMTATPLREDNRDTYRYFGNPI 357
Query: 251 -----------KFNKPYKVFKTST---------------FRSNLFYDVIFD--DL----- 277
F PY+V + + D + D
Sbjct: 358 YTYSLRQGIDDGFLAPYRVHRVISEVDAAGWRPSKGDVDRFGREIPDGEYQTKDFERVIA 417
Query: 278 LKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKHERSRVQESFM 337
LK + + + + ++ I++C +EH ++ AL +N + +
Sbjct: 418 LKARTDAFAKHLTDFMKRTDR-FAKTIVFCVDQEHADEMRRAL-NNLNSDLSRKHPDYVA 475
Query: 338 R 338
R
Sbjct: 476 R 476
>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*
Length = 556
Score = 38.0 bits (87), Expect = 0.005
Identities = 51/330 (15%), Positives = 94/330 (28%), Gaps = 52/330 (15%)
Query: 156 EELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLA-YIVVDEAHCVSEWGHDFRPT 214
++RLVK RI + + L++ + + L+ D E
Sbjct: 222 IDVRLVKRRIHNPFAAIISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQR 281
Query: 215 YRRLGELRQFTGNSIPIIALTATAEPSVK----------QDIISVLKFNKPYKVFKTSTF 264
RL +L S AL E K II L + + +
Sbjct: 282 KCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGP 341
Query: 265 RSNL--FYDVIFDDLLKDSYAHVKEFIEKC-----------LGKDNKANNCGIIYCRTRE 311
+ L F + + A K+ + +++ +TR
Sbjct: 342 YTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRA 401
Query: 312 HTTDLADAL------------------RRKVNKHERSRVQ----ESFMRGEIN-VITATI 348
+ L + RR Q ++F + N ++ AT
Sbjct: 402 LVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATS 461
Query: 349 SFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG-----LQSYCRIYHSEHSKKSLE 403
GID VV + ++ Q GR G + S + +E + E
Sbjct: 462 VADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSKCILVTSKTEVVENEKCNRYKE 521
Query: 404 YVIKTDTSTKREQLELKFKNYLSMLEYCEQ 433
++ ++ E F + L+ E+
Sbjct: 522 EMMNKAVEKIQKWDEETFAKKIHNLQMKER 551
>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold,
winged-helix-turn-helix, antiparallel-coiled-COI domain,
ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces
cerevisiae}
Length = 1108
Score = 38.3 bits (88), Expect = 0.006
Identities = 23/122 (18%), Positives = 41/122 (33%), Gaps = 22/122 (18%)
Query: 283 AHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKH-------ERSRVQES 335
+ + + + + R + LRR + H + ++
Sbjct: 473 EALTKIFNNAIALLPETD-------RELPQIKHILPLLRRGIGIHHSGLLPILKEVIEIL 525
Query: 336 FMRGEINVITATISFGMGID--------RQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ 387
F G + V+ AT +F +G++ ++ S Y Q SGRAGR GL
Sbjct: 526 FQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLD 585
Query: 388 SY 389
Sbjct: 586 DR 587
Score = 32.1 bits (72), Expect = 0.43
Identities = 11/33 (33%), Positives = 13/33 (39%), Gaps = 5/33 (15%)
Query: 44 FGFDSFKCELQKKAIRHILLRTHDIFVSMPTGA 76
F D F Q AI + R + VS T A
Sbjct: 183 FTLDPF----QDTAISC-IDRGESVLVSAHTSA 210
>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase,
tramp, exosome, DEAD, nucleotide-binding; HET: ADP;
2.90A {Saccharomyces cerevisiae}
Length = 1010
Score = 38.2 bits (88), Expect = 0.006
Identities = 23/122 (18%), Positives = 41/122 (33%), Gaps = 22/122 (18%)
Query: 283 AHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKH-------ERSRVQES 335
+ + + + + R + LRR + H + ++
Sbjct: 375 EALTKIFNNAIALLPETD-------RELPQIKHILPLLRRGIGIHHSGLLPILKEVIEIL 427
Query: 336 FMRGEINVITATISFGMGID--------RQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ 387
F G + V+ AT +F +G++ ++ S Y Q SGRAGR GL
Sbjct: 428 FQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLD 487
Query: 388 SY 389
Sbjct: 488 DR 489
Score = 32.1 bits (72), Expect = 0.46
Identities = 11/33 (33%), Positives = 13/33 (39%), Gaps = 5/33 (15%)
Query: 44 FGFDSFKCELQKKAIRHILLRTHDIFVSMPTGA 76
F D F Q AI + R + VS T A
Sbjct: 85 FTLDPF----QDTAISC-IDRGESVLVSAHTSA 112
>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET:
ANP; 2.14A {Mus musculus}
Length = 555
Score = 37.6 bits (86), Expect = 0.008
Identities = 24/166 (14%), Positives = 49/166 (29%), Gaps = 28/166 (16%)
Query: 296 DNKANNCGIIYCRTREHTTDLADALRRKVN-----------------------KHERSRV 332
K I++ +TR L + ++ +
Sbjct: 385 HLKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVL 444
Query: 333 QESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG-----LQ 387
+ G+ N++ AT GID V+ + ++ Q GR L
Sbjct: 445 EAFRASGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGRGRARDSKCFLLT 504
Query: 388 SYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQ 433
S + E + E ++ + E+KF + ++ E+
Sbjct: 505 SSADVIEKEKANMIKEKIMNESILRLQTWDEMKFGKTVHRIQVNEK 550
>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA
compl protease/ntpase/helicase, hydrolase; 1.95A
{Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4a92_A*
1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A*
3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A
Length = 666
Score = 37.3 bits (86), Expect = 0.009
Identities = 32/243 (13%), Positives = 57/243 (23%), Gaps = 61/243 (25%)
Query: 181 HYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEP 240
+L I+ DE H +I I
Sbjct: 307 KFLADGGCSGGAYDIIICDECHS--------------------TDSTTILGIGT------ 340
Query: 241 SVKQDIISVLKFNKPYKVFKTS-TFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKA 299
++ + V + T ++ + + S F K + +
Sbjct: 341 -----VLDQAETAGARLVVLATATPPGSVTVPHPNIEEVALSNTGEIPFYGKAIPIEAIR 395
Query: 300 NNCGIIYCRTREHTTDLADALRRKVNKHE---RSRVQESFMRGEINVITAT--ISFGMGI 354
+I+C +++ +LA L R V+ AT + G
Sbjct: 396 GGRHLIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSVIPTIGDVVVVATDALMTGYTG 455
Query: 355 DRQNVRFVVHWG---------------------MPSSIPAYYQESGRAGRDGLQSYCRIY 393
D V+ +P + Q GR GR Y +
Sbjct: 456 D---FDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGRGRRGIYRFVT 512
Query: 394 HSE 396
E
Sbjct: 513 PGE 515
>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea,
helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16
c.37.1.16 e.10.1.1 PDB: 1gl9_B*
Length = 1054
Score = 37.0 bits (86), Expect = 0.012
Identities = 29/100 (29%), Positives = 46/100 (46%), Gaps = 16/100 (16%)
Query: 279 KDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNK----HERSRVQE 334
+S + + +EK LG GIIY RT E ++ ++L+ K + E
Sbjct: 261 DESISTLSSILEK-LGTG------GIIYARTGEEAEEIYESLKNKFRIGIVTATKKGDYE 313
Query: 335 SFMRGEINVITATISF-GM---GIDR-QNVRFVVHWGMPS 369
F+ GEI+ + T + G G+D + +RF V G PS
Sbjct: 314 KFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPS 353
>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.40A {Anas platyrhynchos}
Length = 797
Score = 36.5 bits (83), Expect = 0.016
Identities = 22/161 (13%), Positives = 44/161 (27%), Gaps = 32/161 (19%)
Query: 296 DNKANNCGIIYCRTREHTTDLADAL------------------RRKVNKHERSRVQ---- 333
+++ +TR + L + RR Q
Sbjct: 627 RYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVL 686
Query: 334 ESFMRGEIN-VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYC-- 390
++F + N ++ AT GID VV + ++ Q GR G +
Sbjct: 687 DAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSKCILVT 746
Query: 391 -------RIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNY 424
+ + ++ + ++ E K N
Sbjct: 747 SKTEVVENEKCNRYKEEMMNKAVEKIQKWDEETFAKKIHNL 787
>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation,
exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB:
4a4k_A
Length = 997
Score = 36.0 bits (82), Expect = 0.031
Identities = 31/155 (20%), Positives = 57/155 (36%), Gaps = 22/155 (14%)
Query: 283 AHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKHE-------RSRVQES 335
+ + FIEK + + K + R L R + H + ++
Sbjct: 368 SQIHMFIEKSITRLKKED-------RDLPQILKTRSLLERGIAVHHGGLLPIVKELIEIL 420
Query: 336 FMRGEINVITATISFGMGID--------RQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ 387
F +G I V+ AT +F MG++ + + + + Q +GRAGR GL
Sbjct: 421 FSKGFIKVLFATETFAMGLNLPTRTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLD 480
Query: 388 SYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFK 422
S + ++ K T +L+ +F+
Sbjct: 481 STGTVIVMAYNSPLSIATFKEVTMGVPTRLQSQFR 515
>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein;
HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19
c.37.1.19 PDB: 2fzl_A*
Length = 472
Score = 35.2 bits (81), Expect = 0.041
Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 5/57 (8%)
Query: 304 IIYCRTREHTTDLADALRR-----KVNKHERSRVQESFMRGEINVITATISFGMGID 355
II+ R E ++ + ++ ER + E F G I ++ GID
Sbjct: 353 IIFTRHNELVYRISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGID 409
>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.70A {Anas platyrhynchos}
Length = 936
Score = 34.9 bits (79), Expect = 0.063
Identities = 20/172 (11%), Positives = 48/172 (27%), Gaps = 34/172 (19%)
Query: 284 HVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRR--------------------- 322
+ ++ + +++ +TR + L +
Sbjct: 617 ELVCILDDAYRYNP--QTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQT 674
Query: 323 -KVNKHERSRVQESFMRGEIN-VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGR 380
+ + V ++F + N ++ AT GID VV + ++ Q GR
Sbjct: 675 TGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR 734
Query: 381 AGRDGLQSYC---------RIYHSEHSKKSLEYVIKTDTSTKREQLELKFKN 423
G + + + ++ + ++ E K N
Sbjct: 735 GRAAGSKCILVTSKTEVVENEKCNRYKEEMMNKAVEKIQKWDEETFAKKIHN 786
>2r25_B Osmosensing histidine protein kinase SLN1; alpha5-BETA5, response
regulator, four helix bundle, histidine phosphotransfer
(HPT) protein; 1.70A {Saccharomyces cerevisiae} SCOP:
c.23.1.1 PDB: 1oxk_B 1oxb_B
Length = 133
Score = 32.1 bits (74), Expect = 0.11
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 220 ELRQFTGNSIPIIALTATAEPS 241
+R+ G + PI+ALTA A+ S
Sbjct: 73 MIRRDLGYTSPIVALTAFADDS 94
>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate
immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*
Length = 696
Score = 33.4 bits (75), Expect = 0.18
Identities = 13/69 (18%), Positives = 25/69 (36%), Gaps = 1/69 (1%)
Query: 318 DALRRKVNKHERSRVQESF-MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQ 376
+ + + ++F G+ N++ AT GID V+ + ++ Q
Sbjct: 438 TNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQ 497
Query: 377 ESGRAGRDG 385
GR G
Sbjct: 498 TRGRGRARG 506
>3mm4_A Histidine kinase homolog; receiver domain, CKI1, cytokinin
signaling, ROS fold, CHEY-like, transferase; 2.00A
{Arabidopsis thaliana} PDB: 3mmn_A
Length = 206
Score = 31.7 bits (72), Expect = 0.34
Identities = 6/23 (26%), Positives = 12/23 (52%)
Query: 216 RRLGELRQFTGNSIPIIALTATA 238
R + ++ + G PIIA++
Sbjct: 139 REIRKVEKSYGVRTPIIAVSGHD 161
>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A
{Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19
c.37.1.19
Length = 780
Score = 32.2 bits (74), Expect = 0.42
Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 11/65 (16%)
Query: 138 QLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIV 197
+ L++ T +E + I LR +I ++ T H L+Q V + L ++
Sbjct: 447 HVALLIGATTPSEKEKIKSGLR--NGQIDVVIGT---------HALIQEDVHFKNLGLVI 495
Query: 198 VDEAH 202
+DE H
Sbjct: 496 IDEQH 500
>1tlt_A Putative oxidoreductase (virulence factor MVIM HO; structural
genomics, NYSGXRC, PSI, protein structure initiative;
2.70A {Escherichia coli} SCOP: c.2.1.3 d.81.1.5
Length = 319
Score = 30.8 bits (70), Expect = 0.84
Identities = 9/83 (10%), Positives = 21/83 (25%)
Query: 76 AVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSD 135
A+ L G S + A +L G + +T
Sbjct: 174 ALWLSGGKASLDGGTLLTNDAGEMLFAEHHFSAGPLQITTCMHRRAGSQRETVQAVTDGA 233
Query: 136 LYQLELIVSGQTKTENKAILEEL 158
L + + + + + + +
Sbjct: 234 LIDITDMREWREERGQGVVHKPI 256
>3m6m_D Sensory/regulatory protein RPFC; RPFF, REC, enoyl-COA hydratase,
lyase-transferase COMP; 2.50A {Xanthomonas campestris
PV}
Length = 143
Score = 29.5 bits (67), Expect = 1.2
Identities = 4/23 (17%), Positives = 11/23 (47%)
Query: 216 RRLGELRQFTGNSIPIIALTATA 238
++L ++ P++ L+A
Sbjct: 78 KQLRVMQASGMRYTPVVVLSADV 100
>4djd_C C/Fe-SP, corrinoid/iron-sulfur protein large subunit; TIM barrel,
rossmann fold, B12-dependent methyltransferase; HET:
B12; 2.38A {Moorella thermoacetica} PDB: 4dje_C* 4djf_C*
Length = 446
Score = 29.6 bits (66), Expect = 2.2
Identities = 21/86 (24%), Positives = 33/86 (38%), Gaps = 10/86 (11%)
Query: 196 IVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEP----------SVKQD 245
+V+D + RRL ++F PIIALT A P K
Sbjct: 229 LVLDPGARETSRAIADFTQIRRLAIKKRFRSFGYPIIALTTAANPLDEVLQAVNYVTKYA 288
Query: 246 IISVLKFNKPYKVFKTSTFRSNLFYD 271
+ VL+ + + ++R NL+ D
Sbjct: 289 SLVVLRTDAKEHLLPLLSWRQNLYTD 314
>2ayx_A Sensor kinase protein RCSC; two independent structural domains,
transferase; NMR {Escherichia coli} SCOP: c.23.1.1
c.23.1.6 PDB: 2ayz_A 2ayy_A
Length = 254
Score = 28.5 bits (64), Expect = 3.7
Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 220 ELRQFTGNSIPIIALTATAEPSVKQ 244
+RQ G ++P+I +TA A KQ
Sbjct: 194 RIRQL-GLTLPVIGVTANALAEEKQ 217
>3kht_A Response regulator; PSI-II, 11023K, structural genomics, Pro
structure initiative, NEW YORK SGX research center for
STRU genomics, nysgxrc; 2.10A {Hahella chejuensis}
Length = 144
Score = 27.6 bits (62), Expect = 4.2
Identities = 6/23 (26%), Positives = 9/23 (39%), Gaps = 5/23 (21%)
Query: 216 RRLGELRQFTGNSIPIIALTATA 238
R+ G + PI+ LT
Sbjct: 74 RKPGANQH-----TPIVILTDNV 91
>3luf_A Two-component system response regulator/ggdef domain protein;
structural genomics, ASA_2441, PSI-2, protein structure
initiative; HET: MSE; 1.76A {Aeromonas salmonicida} PDB:
3mf4_A*
Length = 259
Score = 28.4 bits (64), Expect = 4.5
Identities = 4/26 (15%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 220 ELRQ-FTGNSIPIIALTATAEPSVKQ 244
LR+ ++ + II ++ + + +
Sbjct: 190 MLRERYSKQQLAIIGISVSDKRGLSA 215
>3dmn_A Putative DNA helicase; APC89291.2, lactobacillus plantarum WCFS1,
STR genomics, PSI-2, midwest center for structural
genomics; HET: MSE; 1.66A {Lactobacillus plantarum}
Length = 174
Score = 27.8 bits (62), Expect = 5.0
Identities = 10/70 (14%), Positives = 31/70 (44%), Gaps = 1/70 (1%)
Query: 283 AHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKHERSRVQESFMRGEIN 342
A V + +++ D++ + II ++ L AL+ + + + + + +
Sbjct: 45 AGVDQVVDQLAMNDSERDTTAII-GKSLAECEALTKALKARGEQVTLIQTENQRLAPGVI 103
Query: 343 VITATISFGM 352
V+ + ++ G+
Sbjct: 104 VVPSFLAKGL 113
>2qvg_A Two component response regulator; NYSGXRC, PSI-2, structural
genomics, protein structure initiative; 1.50A
{Legionella pneumophila subsp}
Length = 143
Score = 27.6 bits (62), Expect = 5.1
Identities = 5/20 (25%), Positives = 8/20 (40%), Gaps = 3/20 (15%)
Query: 228 SIPIIALTATAEPSVKQDII 247
I + LTA +D +
Sbjct: 89 DIEVFVLTAAYTS---KDKL 105
>1mb3_A Cell division response regulator DIVK; signal transduction protein,
structural proteomics in europe, spine, structural
genomics; 1.41A {Caulobacter vibrioides} SCOP: c.23.1.1
PDB: 1m5u_A 1mav_A 1mb0_A 1m5t_A
Length = 124
Score = 27.1 bits (61), Expect = 6.8
Identities = 6/11 (54%), Positives = 9/11 (81%)
Query: 228 SIPIIALTATA 238
IP++A+TA A
Sbjct: 75 HIPVVAVTAFA 85
>3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein S
initiative, structural genomics; 2.59A {Cytophaga
hutchinsonii}
Length = 146
Score = 27.3 bits (61), Expect = 6.8
Identities = 4/26 (15%), Positives = 10/26 (38%)
Query: 216 RRLGELRQFTGNSIPIIALTATAEPS 241
+ Q N + L+++ +P
Sbjct: 80 DLFKQHFQPMKNKSIVCLLSSSLDPR 105
>2y35_A LD22664P; hydrolase-DNA complex, RNA degradation, exonuclease
5'-3', R interference; 3.20A {Drosophila melanogaster}
Length = 1140
Score = 28.0 bits (61), Expect = 7.3
Identities = 34/255 (13%), Positives = 67/255 (26%), Gaps = 17/255 (6%)
Query: 183 LLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSV 242
L H + + L V + + R LG LR++ +
Sbjct: 213 LCTHELHFVVLREEVKFGRNVKRTSVEETRFFLLHLGLLREYLELEFDALR-----TDEH 267
Query: 243 KQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNC 302
K DI ++ + F +L I + L Y G N N
Sbjct: 268 KLDIAQLIDDWVLMGFLVGNDFIPHLPCLHISSNALPLLYRTYIGIYPTLGGNIN--ENG 325
Query: 303 GIIYCRTREHTTDLADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFV 362
+ R + + L + +H + + M +
Sbjct: 326 KLNLRRLQIFISALTEVELDHFKEHADDLKYMNNKSEAFD---------MDVGEITESQN 376
Query: 363 VHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE-HSKKSLEYVIKTDTSTKREQLELKF 421
+ + + I + + E + K Y K E +E
Sbjct: 377 LDSDLGALINKSMLLYDDDSEEDCSDENAVLLKEFQNYKRNFYRNKFKRDPNDELIEELC 436
Query: 422 KNYLSMLEYCEQGYF 436
+Y++ L++ Y+
Sbjct: 437 HHYVNALQWVLDYYY 451
>4evf_A Alpha-1 giardin, giardin subunit alpha-1; annexin, calcium-binding
protein, membrane-binding protein, binding protein;
1.90A {Giardia intestinalis} PDB: 4evh_A
Length = 295
Score = 27.5 bits (61), Expect = 8.0
Identities = 7/34 (20%), Positives = 8/34 (23%), Gaps = 1/34 (2%)
Query: 386 LQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLEL 419
Y KK L D K + L
Sbjct: 107 WHETVAAYTRMF-KKPLVEDFMKDVGRKEDWCLL 139
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.321 0.136 0.395
Gapped
Lambda K H
0.267 0.0639 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,648,080
Number of extensions: 399995
Number of successful extensions: 1136
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1075
Number of HSP's successfully gapped: 78
Length of query: 444
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 347
Effective length of database: 3,993,456
Effective search space: 1385729232
Effective search space used: 1385729232
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 (21.9 bits)
S2: 59 (26.7 bits)