RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= 537021.9.peg.410_1
(952 letters)
>1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase,
hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli}
SCOP: c.37.1.19 c.37.1.19 c.52.1.24 PDB: 3k70_B*
Length = 1180
Score = 163 bits (412), Expect = 2e-40
Identities = 129/873 (14%), Positives = 278/873 (31%), Gaps = 114/873 (13%)
Query: 96 LKEKLKKSQDEFIKIRDRFNTYKMFKSTLASLTLAKYLNAHYEEAKKKNCVLDFEDLIIN 155
K + + + D+ + L + K++ L F+D++
Sbjct: 298 TKAGGETPRHPLFEAIDQLLAEPLSIRDLVITRALAEIRETVAREKRRRGELGFDDMLSR 357
Query: 156 TNDLLKKRDVSAWIRYKIDQEINHILIDEVQDTSLIQWEVIRSLTEDFFVGKNTHSSPRT 215
+ + + + I +IDE QDT Q+ + R + H
Sbjct: 358 LDSA-LRSESGEVLAAAIRTRFPVAMIDEFQDTDPQQYRIFRRIWH--------HQPETA 408
Query: 216 LFAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFSIIELPLSFRSTADILTVVD 275
L +GD KQ+IY+F GA+ ++ + L ++RS ++ V+
Sbjct: 409 LLLIGDPKQAIYAFRGADIFTYMKARSEVHAH----------YTLDTNWRSAPGMVNSVN 458
Query: 276 KVFSIPENAQGLSEDSTTTIRHRSSRIGQVGTVQLWEQVVSQHDSQCNPQQESWTSYFDS 335
K+FS ++A E ++ + + + P + W +S
Sbjct: 459 KLFSQTDDAFMFREIPFIPVKSAGK----------NQALRFVFKGETQPAMKMWLMEGES 508
Query: 336 LPQESSASILARRIAYTISNMI-----GTDTIFSNGKKRVIQAKDILVLVRKRKDTPLIT 390
S +A+ A I + + G + + R ++A DI VLVR R++ +
Sbjct: 509 CGVGDYQSTMAQVCAAQIRDWLQAGQRGEALLMNGDDARPVRASDISVLVRSRQEAAQVR 568
Query: 391 FLTRFLKNDYKISVVGNDRFILTDHLAIKDLMALGRFILSQEDDLSFVCMLKSPLFNFSE 450
L+ V ++R + + L ++++ L + +++ E + + L + + +
Sbjct: 569 DALTLLEIPS---VYLSNRDSVFETLEAQEMLWLLQAVMTPERENTLRSALATSMMGLNA 625
Query: 451 DDIFKICTQRHETETVYEYIQKFANCGISKFQHVIKYIHELIHIAQFCSPHDFFTLILGA 510
DI + H + V E + + + + + S + +L
Sbjct: 626 LDIETLNNDEHAWDVVVEEFDGYRQ--------IWRKRGVMPMLRALMSARNIAENLLAT 677
Query: 511 KKGRQQFISRFGNEVIDVLDEFLNFTLRNEQNSYSSLQELISELEQYPPTIKRAHSANHN 570
G ++ I L + L +E L + I E + + + ++ +
Sbjct: 678 AGGERRLTDI---LHISELLQEAGTQLESEHALVRWLSQHILEPDSNASSQQMRLESDKH 734
Query: 571 EVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIKKMHIMPSLNDDPGIPIWIPQSKSRNN 630
V+I+T+H +KGLE P+V+L + + +D + N
Sbjct: 735 LVQIVTIHKSKGLEYPLVWLPFITNFRVQEQAF--------YHDRHSFEAVLD-----LN 781
Query: 631 IVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLII--CKHSNTSNEKKSNQRTWYDMVYDS 688
+ + + E RLLYV +TR+ + +KK + +
Sbjct: 782 AAPESVDLAEAERLAEDLRLLYVALTRSVWHCSLGVAPLVRRRGDKKGDTDVHQSALGRL 841
Query: 689 FHNDERVKKIKLTNSINKDEWIAYEWSTHH-PENTPLEREETIKQLMDEQKIPKKLFSPI 747
E L I W T +N P + + ++ + + +
Sbjct: 842 LQKGEPQDAAGLRTCIEALCDDDIAWQTAQTGDNQPWQVNDVSTAELNAKTLQRLPGDNW 901
Query: 748 K-----------NDINEPYILNPSTIDTKGKTNLESLLSDNQTF----NRGLIIHKLLQV 792
+ + I + + + +E F + G +H L +
Sbjct: 902 RVTSYSGLQQRGHGIAQDLMPRLDVDAAGVASVVEEPTLTPHQFPRGASPGTFLHSLFED 961
Query: 793 I-FTLPEHKR-----------------------KNFITSYCTKNAKLWPAKEYKNLLLSI 828
+ FT P + + + +N + +
Sbjct: 962 LDFTQPVDPNWVREKLELGGFESQWEPVLTEWITAVLQAPLNETGVSLSQLSARNKQVEM 1021
Query: 829 TRLLENPMMTTAMSCDSYSEVSVSGKINCPKKD-----IIISGRIDQISISQQNIFIFEY 883
L A D+ CP + ++ G ID + + ++ +Y
Sbjct: 1022 EFYLPISEPLIASQLDTLIRQFDPLSAGCPPLEFMQVRGMLKGFIDLVFRHEGRYYLLDY 1081
Query: 884 KTHHHVPQEIEHIPYTHIAQLSIYEKILKDSYP 916
K+ + + ++ YT A + + Y
Sbjct: 1082 KS-NWLGEDSSA--YTQQA---MAAAMQAHRYD 1108
>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP-
binding, DNA-binding; 2.50A {Geobacillus
stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB:
1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C*
2pjr_B*
Length = 724
Score = 146 bits (369), Expect = 2e-35
Identities = 125/601 (20%), Positives = 228/601 (37%), Gaps = 119/601 (19%)
Query: 81 QKNIITQEINKKSPDLKE-KLKKSQDEFIKIRDRFNTYKMFKSTLASLT--LAKYLNAHY 137
Q +++ + +K+ D K+ + + ++ + F ++ + + Y
Sbjct: 121 QLSVMKTILKEKNIDPKKFEPRTILGTISAAKNELLPPEQFAKRASTYYEKVVSDVYQEY 180
Query: 138 EEAKKKNCVLDFEDLIINTNDLLKKRDVSAWIRYKIDQEINHILIDEVQDTSLIQWEVIR 197
++ +N LDF+DLI+ T L + + + + +I IDE QDT+ Q+ +++
Sbjct: 181 QQRLLRNHSLDFDDLIMTTIQLFDRVP---DVLHYYQYKFQYIHIDEYQDTNRAQYTLVK 237
Query: 198 SLTEDFFVGKNTHSSPRTLFAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFSI 257
L E F + + AVGD QSIY + GA+ + +L +R +
Sbjct: 238 KLAERF----------QNICAVGDADQSIYRWRGADIQNILSFER--------DYPNAKV 279
Query: 258 IELPLSFRSTADILTVVDKVFSIPENAQGLSEDSTTTIRHRSSRIGQVGTVQLWEQVVSQ 317
I L ++RST IL ++V I H +R + + E
Sbjct: 280 ILLEQNYRSTKRILQAANEV-----------------IEHNVNRKPKRIWTENPEGKPIL 322
Query: 318 HDSQCNPQQESWTSYFDSLPQESSASILARRIAYTISNMIGTDTIFSNGKKRVIQAKDIL 377
+ N E A+ +A I + ++ + +D
Sbjct: 323 YYEAMNEADE------------------AQFVAGRIREAV---------ERGERRYRDFA 355
Query: 378 VLVRKRKDTPLITFLTRFLKNDYKISVVGNDRFILTDHLAIKDLMALGRFILSQEDDLSF 437
VL R + ++ LK + +VG +F D IKD++A R I + +DDLS
Sbjct: 356 VLYRTNAQSRVME--EMLLKANIPYQIVGGLKFY--DRKEIKDILAYLRVIANPDDDLSL 411
Query: 438 VCMLKSPLFNFSEDDIFKICTQ-RHETETVYEYIQKFANCGIS-----KFQHVIKYIHEL 491
+ ++ P I K+ +++E + + G+ + +
Sbjct: 412 LRIINVPKRGIGASTIDKLVRYAADHELSLFEALGELEMIGLGAKAAGALAAFRSQLEQW 471
Query: 492 IHIAQFCSPHDFFTLILGAKKGRQQFISR---FGNEVIDVLDEFLNFTLRNEQ-NSYSSL 547
+ ++ S + +L R+ + ++ LDEFL+ T E + SL
Sbjct: 472 TQLQEYVSVTELVEEVLDKSGYREMLKAERTIEAQSRLENLDEFLSVTKHFENVSDDKSL 531
Query: 548 QELISELEQYPPTIKRA---HSANHNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIK 604
+++L + +A + V +MT+H AKGLE PVVFL+ +F H
Sbjct: 532 IAFLTDLALISDLDELDGTEQAAEGDAVMLMTLHAAKGLEFPVVFLIGMEEGIFPHNR-- 589
Query: 605 KMHIMPSLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLII 664
SL DD + EE RL YVG+TRA ++L++
Sbjct: 590 ------SLEDDDEM--------------------------EEERRLAYVGITRAEEELVL 617
Query: 665 C 665
Sbjct: 618 T 618
>2is6_A DNA helicase II; hydrolase/DNA complex; HET: DNA ADP; 2.20A
{Escherichia coli} PDB: 2is2_A* 2is1_A* 2is4_A*
Length = 680
Score = 135 bits (341), Expect = 4e-32
Identities = 111/601 (18%), Positives = 210/601 (34%), Gaps = 122/601 (20%)
Query: 81 QKNIITQEINKKSPDLKEKLKKSQDEFIKIRDRFNTYKMFKSTLASL--TLAKYLNAHYE 138
Q ++ + I + D K+ + +I + + + + + Y+
Sbjct: 119 QLRLLKRLIKAMNLDEKQWPPRQAMWYINSQKDEGLRPHHIQSYGNPVEQTWQKVYQAYQ 178
Query: 139 EAKKKNCVLDFEDLIINTNDLLKKRDVSAWIRYKIDQEINHILIDEVQDTSLIQWEVIRS 198
EA + ++DF +L++ ++L + I + +IL+DE QDT+ IQ+ IR
Sbjct: 179 EACDRAGLVDFAELLLRAHELWLNKP---HILQHYRERFTNILVDEFQDTNNIQYAWIR- 234
Query: 199 LTEDFFVGKNTHSSPRTLFAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFSII 258
+ VGD+ QSIY + GA+ N +R N I
Sbjct: 235 ---------LLAGDTGKVMIVGDDDQSIYGWRGAQV--------ENIQRFLNDFPGAETI 277
Query: 259 ELPLSFRSTADILTVVDKVFSIPENAQGLSEDSTTTIRHRSSRIGQVGTVQLWEQVVSQH 318
L ++RST++IL+ + + I + + R+G+ +LW
Sbjct: 278 RLEQNYRSTSNILSAANAL-----------------IENNNGRLGK----KLWTD----- 311
Query: 319 DSQCNPQQESWTSYFDSLPQESSASILARRIAYTISNMIGTDTIFSNGKKRVIQAKDILV 378
+ + S F+ L + AR + I + +
Sbjct: 312 --GADGEPISLYCAFNELDE-------ARFVVNRIKTWQ----------DNGGALAECAI 352
Query: 379 LVRKRKDTPLITFLTRFLKNDYKISVVGNDRFILTDHLAIKDLMALGRFILSQEDDLSFV 438
L R + ++ L+ + G RF + IKD ++ R I+++ DD +F
Sbjct: 353 LYRSNAQSRVLE--EALLQASMPYRIYGGMRFF--ERQEIKDALSYLRLIVNRNDDAAFE 408
Query: 439 CMLKSPLFNFSEDDIFKICTQRHETETVYEY----------IQKFANCGISKFQHVIKYI 488
++ +P + + + + + + A + +F +I +
Sbjct: 409 RVVNTPTRGIGDRTLDVVRQTSRDRQLTLWQACRELLQEKALAGRAASALQRFMELIDAL 468
Query: 489 HELIHIAQFCSPHDFFTLILGAKKGRQQFISRFGNEVIDVLDEFLN----FTLRNEQNSY 544
+ D G + +Q G I+ L+E + F+ E
Sbjct: 469 AQETADMPLHVQTDRVIKDSGLRTMYEQEKGEKGQTRIENLEELVTATRQFSYNEEDEDL 528
Query: 545 SSLQELISELEQYPPTIKRAHSANHNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIK 604
LQ +S + + V++MT+H+AKGLE P VF+V +F +
Sbjct: 529 MPLQAFLSHAALE--AGEGQADTWQDAVQLMTLHSAKGLEFPQVFIVGMEEGMFPSQM-- 584
Query: 605 KMHIMPSLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLII 664
SL++ + EE RL YVG+TRA +L +
Sbjct: 585 ------SLDEGGRL--------------------------EEERRLAYVGVTRAMQKLTL 612
Query: 665 C 665
Sbjct: 613 T 613
>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex
(helicase/DNA), DNA unwinding, hydrolase/DNA complex;
HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19
c.37.1.19
Length = 673
Score = 112 bits (280), Expect = 4e-25
Identities = 96/598 (16%), Positives = 182/598 (30%), Gaps = 121/598 (20%)
Query: 82 KNIITQEINKKSPDLKEKLKKSQDEFIKIRDRFNTYKMFKSTLASLTLAKYLNAHYEEAK 141
K + I L++ + + ++ + Y Y+
Sbjct: 118 KELTEGLIEDDKVLLQQLISTISNWKNDLKTPSQAAASAIGERDRIFAHCY--GLYDAHL 175
Query: 142 KKNCVLDFEDLIINTNDLLKKRDVSAWIRYKIDQEINHILIDEVQDTSLIQWEVIRSLTE 201
K VLDF+DLI+ LL+ + +R + +I ++L+DE QDT+ Q+
Sbjct: 176 KACNVLDFDDLILLPTLLLQANE---EVRKRWQNKIRYLLVDEYQDTNTSQY-------- 224
Query: 202 DFFVGKNTHSSPRTLFAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFSIIELP 261
+ K S VGD+ QSIYS+ GA P N + +I+L
Sbjct: 225 --ELVKLLVGSRARFTVVGDDDQSIYSWRGARP--------QNLVLLSQDFPALKVIKLE 274
Query: 262 LSFRSTADILTVVDKVFSIPENAQGLSEDSTTTIRHRSSRIGQVGTVQLWEQVVSQHDSQ 321
++RS+ IL + + I + + +L + S
Sbjct: 275 QNYRSSGRILKAANIL-----------------IANNPHVFEKRLFSELGYGAELKVLSA 317
Query: 322 CNPQQESWTSYFDSLPQESSASILARRIAYTISNMIGTDTIFSNGKKRVIQAKDILVLVR 381
N + E+ + + ++ Q KD +L R
Sbjct: 318 NNEEHEAERVTGE---------------------------LIAHHFVNKTQYKDYAILYR 350
Query: 382 KRKDTPLITFLTRFLKNDYKISVVGNDRFILTDHLAIKDLMALGRFILSQEDDLSFVCML 441
+ + ++N + G F IKDL+A R + + +DD +F+ ++
Sbjct: 351 GNHQSRVFE--KFLMQNRIPYKISGGTSFF--SRPEIKDLLAYLRVLTNPDDDSAFLRIV 406
Query: 442 KSPLFNFSEDDIFKICTQRHETETVYEYIQKFANCGISKFQHVIKYIHELIHIAQFCSPH 501
+P + K+ + + + H
Sbjct: 407 NTPKREIGPATLKKLGEWAMTRNKSMFTASFDMGLSQTLSGRGYEALTRFTHWLAEIQRL 466
Query: 502 DFFTLI---------------LGAKKGRQQFISRFGNEVIDVLDEFLNFTLRNEQNSYSS 546
I L + V + +E + +
Sbjct: 467 AEREPIAAVRDLIHGMDYESWLYETSPSPKAAEMRMKNVNQLFSWMTEMLEGSELDEPMT 526
Query: 547 LQELISELEQYPPTIKRAHSANHNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIKKM 606
L ++++ + ++V++MT+H +KGLE P V++V H+
Sbjct: 527 LTQVVTRFTLRDMMERGESEEELDQVQLMTLHASKGLEFPYVYMVGMEEGFLPHQ----- 581
Query: 607 HIMPSLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLII 664
+ + +E RL YVG+TRA +L
Sbjct: 582 ------------------------------SSIDEDNIDEERRLAYVGITRAQKELTF 609
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 76.5 bits (188), Expect = 2e-14
Identities = 106/706 (15%), Positives = 193/706 (27%), Gaps = 303/706 (42%)
Query: 287 LSEDSTTTIRHRSSRIGQVGTVQLWEQVVSQHDSQCNPQQESWTSYFDSLPQESSASILA 346
LS S + + + + QL EQ P + D P + A ++
Sbjct: 11 LSHGSLEHVLLVPTASFFIAS-QLQEQFNKILPE---PTEGFA---ADDEP-TTPAELVG 62
Query: 347 RRIAYTISNMIGTDTIFSNGKKRVIQAKDILVLVRKRKDTPLITFLTRFLK-NDYKI-SV 404
+ + Y + + Q +L L L F +L+ ND I ++
Sbjct: 63 KFLGYVS------SLVEPSKVG---QFDQVLNLC-------LTEFENCYLEGND--IHAL 104
Query: 405 VG-----NDRFILTDHLAIKD----LMALGRFILSQEDDLSFVCMLKSPLFNFSEDDIFK 455
ND ++ IK+ + R + + S LF + +
Sbjct: 105 AAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSN---------SALFRAVGEGNAQ 155
Query: 456 I--------CTQRHETE-----TVY-----EYIQKFANC--GISK--------FQH---V 484
+ T + E Y + I+ A + + F +
Sbjct: 156 LVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNI 215
Query: 485 IKYIHE---------------------LIHIAQFC--------SPHDFFTLILGAKKGRQ 515
++++ +I +A + +P + + + GA G
Sbjct: 216 LEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGAT-GHS 274
Query: 516 Q------FIS------RFGNEVIDVLDEFLNFT-LRNEQNSY--SSLQELISELEQYPPT 560
Q I+ F V + L F +R +Y +SL PP+
Sbjct: 275 QGLVTAVAIAETDSWESFFVSVRKAI-TVLFFIGVRC-YEAYPNTSL----------PPS 322
Query: 561 IKRAHSANHNE--------VRIMTVHTAKGLESPVV--FLVDTGSQVFSHKHIKKMHIMP 610
I S +NE + L V ++ T S + + K + I
Sbjct: 323 I-LEDSLENNEGVPSPMLSIS--------NLTQEQVQDYVNKTNSHLPAGKQV---EI-- 368
Query: 611 SLNDDPGIPIWIPQSKSRNNIVS-------DLIKHLKKSTQEEYNRLLYVGMTRASDQLI 663
SL + +N +VS L L+K DQ
Sbjct: 369 SLVNGA-----------KNLVVSGPPQSLYGLNLTLRK-----------AKAPSGLDQSR 406
Query: 664 ICKHSNTSNEKKSNQRTWYDMVYDSFHNDERVKKIKLTNS---INKDEWIAYEWSTHHPE 720
I S +R K+K +N + ++ P
Sbjct: 407 I-PFS---------ER-----------------KLKFSNRFLPV----------AS--PF 427
Query: 721 NTP-LER-EETIKQLMDEQKI---PKKLFSPIKNDINEPYILNPSTIDTKGKTNLESLLS 775
++ L + I + + + + K + P+ Y DT ++L L S
Sbjct: 428 HSHLLVPASDLINKDLVKNNVSFNAKDIQIPV-------Y-------DTFDGSDLRVL-S 472
Query: 776 DNQTFNRGLIIHKLLQVIFTLPEHKRKNFITSYCTKNAKLWPAKEYKNLLLSITRLLE-N 834
+ I +++ I LP W T +L+
Sbjct: 473 GS-------ISERIVDCIIRLPVK----------------WE----TTTQFKATHILDFG 505
Query: 835 PMMTTAMSCDSYSEVSVSG-----KINCPKKD-----IIISGRIDQ 870
P SG N KD +I++G +D
Sbjct: 506 PG-------------GASGLGVLTHRN---KDGTGVRVIVAGTLDI 535
Score = 65.0 bits (158), Expect = 7e-11
Identities = 97/611 (15%), Positives = 169/611 (27%), Gaps = 265/611 (43%)
Query: 1 LKNRFGLSLNESYELIYKDLWPLPYFQVSDIN---KYVSLSMETGNPTILKKAQTLQQAS 57
L+ +F L E E D P + K++ + + +
Sbjct: 33 LQEQFNKILPEPTEGFAADDEP-----TTPAELVGKFLGY--------VSSLVEPSKVGQ 79
Query: 58 QTQC-------IEERF-------SLLSSFFLTQKFTP--QKNII----------TQEINK 91
Q E + +L + T K +I + +K
Sbjct: 80 FDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDK 139
Query: 92 KSPD-LKEKLKKSQDEFIKI-----------------RDRFNTYKMFKSTL---ASLTLA 130
KS L + + ++ RD + TY + L ++ TL+
Sbjct: 140 KSNSAL---FRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLS 196
Query: 131 KYLNAHYEEAKKKNCVLDFEDLIINTNDLLKKRDVSAWIRYKIDQ-EINHI--------L 181
+ L +A+K + T L ++ W+ + + +++ L
Sbjct: 197 E-LIRTTLDAEK-----------VFTQGL----NILEWLENPSNTPDKDYLLSIPISCPL 240
Query: 182 IDEVQDTSLIQWEV-----------IRSL----T------------------EDFFVGKN 208
I +Q L + V +RS T E FF +
Sbjct: 241 IGVIQ---LAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFF--VS 295
Query: 209 THSSPRTLFAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFSIIELPLSFRSTA 268
+ LF +G Y P L SI+E
Sbjct: 296 VRKAITVLFFIGVRCYEAY------PNTSLPP---------------SILE--------- 325
Query: 269 DILTVVDKVFSIPENAQG-----LSEDSTTTIRHRSSRIGQVGTVQLWEQVVSQHDSQCN 323
D S+ EN +G LS I + + EQV + + N
Sbjct: 326 D---------SL-ENNEGVPSPMLS------ISNLTQ-----------EQVQDYVN-KTN 357
Query: 324 PQQESWTSYFDSLPQESSASI-L--ARRIAYTISNMIGTDTIFS----NGKKRVIQAKDI 376
S+ LP I L + N++ + S N R +A
Sbjct: 358 -------SH---LPAGKQVEISLVNGAK------NLVVSGPPQSLYGLNLTLRKAKAPSG 401
Query: 377 L----VLVRKRKDTPLITFLTRFLKNDYKISVVGNDRFILTDHLA------IKDLMALGR 426
L + +RK + RFL ++ F + L KDL
Sbjct: 402 LDQSRIPFSERK--LKFS--NRFL----PVAS----PF-HSHLLVPASDLINKDL----- 443
Query: 427 FILSQEDDLSF-VCMLKSPLFN---------FSED---DIFK-ICTQR-H-ETETVYE-- 468
++++SF ++ P+++ S I I ET T ++
Sbjct: 444 ----VKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKAT 499
Query: 469 YIQKFANCGIS 479
+I F G S
Sbjct: 500 HILDFGPGGAS 510
Score = 49.2 bits (117), Expect = 5e-06
Identities = 84/474 (17%), Positives = 142/474 (29%), Gaps = 213/474 (44%)
Query: 10 NESY--EL-----IYKDLWPLPYFQVSDINKYVSLSMETGNPTILKKAQTLQQ-ASQTQC 61
+ Y EL Y L V D+ I A+TL + T
Sbjct: 166 TDDYFEELRDLYQTYHVL-------VGDL--------------IKFSAETLSELIRTTLD 204
Query: 62 IEERFS--------------------LLS---SF---FLTQ--KFTPQKNIITQEINKKS 93
E+ F+ LLS S + Q + ++T ++ +
Sbjct: 205 AEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHY-----VVTAKLLGFT 259
Query: 94 P-DLKEKLK----KSQD----EFIKIRDRFNTYKMFKSTLASLTLAKYLNAHYEEAKKKN 144
P +L+ LK SQ I D +++ F + +K
Sbjct: 260 PGELRSYLKGATGHSQGLVTAVAIAETD---SWESF----------------FVSVRKAI 300
Query: 145 CVLDFEDLIINTNDLLKKRDVSAWIRYKIDQEINHILIDE--VQDTSLIQWE-------V 195
VL F +I + + + + ++D SL E
Sbjct: 301 TVL-F------------------FIGVRCYEAYPNTSLPPSILED-SLENNEGVPSPMLS 340
Query: 196 IRSLTEDF---FVGK-NTH------------SSPRTLFAVGDEKQSIYSFHGAEPKRVLR 239
I +LT++ +V K N+H + + V QS+Y + LR
Sbjct: 341 ISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKN-LVVSGPPQSLYGLN-----LTLR 394
Query: 240 EKR----INQKRATNAGQK--FSIIELPLS--FRS------TADILTVV---DKVFS--- 279
+ + ++Q R + +K FS LP++ F S + I + + F+
Sbjct: 395 KAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKD 454
Query: 280 --IP-------ENAQGLSEDSTTTIRHRSSRIGQVGT--VQLWEQVV---SQH--DSQCN 323
IP + + LS + I + + V+ WE + H D
Sbjct: 455 IQIPVYDTFDGSDLRVLSGSISERI------VDCIIRLPVK-WETTTQFKATHILD---- 503
Query: 324 PQQESWTSYFDSLPQESSA-SILARRIAYTISNMIGTDTIFSNGKKRVIQAKDI 376
F P +S +L R N GT RVI A +
Sbjct: 504 ---------FG--PGGASGLGVLTHR------NKDGTGV-------RVIVAGTL 533
>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase,
hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli}
SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*
Length = 608
Score = 46.6 bits (109), Expect = 3e-05
Identities = 15/119 (12%), Positives = 32/119 (26%), Gaps = 46/119 (38%)
Query: 547 LQELISELEQYPPTIKRAHSANHNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIKKM 606
+ + + +++ + H MTVH ++G E L+
Sbjct: 508 TRVWFAMPDGNIKSVQPSRLPEHETTWAMTVHKSQGSEFDHAALI--------------- 552
Query: 607 HIMPSLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLIIC 665
+P ++ L+Y +TRA +L +
Sbjct: 553 ---------------LPSQRTP----------------VVTRELVYTAVTRARRRLSLY 580
>1w36_C RECC, exodeoxyribonuclease V gamma chain; recombination, helicase,
hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli}
SCOP: c.37.1.19 c.37.1.19 c.52.1.25 PDB: 3k70_C*
Length = 1122
Score = 45.6 bits (107), Expect = 5e-05
Identities = 45/365 (12%), Positives = 99/365 (27%), Gaps = 79/365 (21%)
Query: 367 KKRVIQAKDILVLVRKRKD-TPLITFLTRFLKNDYKISVVGNDRFILTDHLAIKDLMALG 425
+ + +DI+V+V +P I + D + +DR H ++ ++L
Sbjct: 399 EDPTLTPRDIIVMVADIDSYSPFIQAVFGSAPADRYLPYAISDRRARQSHPVLEAFISLL 458
Query: 426 RFILSQEDDLSFVCMLKSPL----FNFSEDDIFKI------------------------- 456
S+ + +L P+ F+ +E+ + +
Sbjct: 459 SLPDSRFVSEDVLALLDVPVLAARFDITEEGLRYLRQWVNESGIRWGIDDDNVRELELPA 518
Query: 457 --------CTQRHETETVYEYIQKFANCGISKFQHVIKYIHELI-HIAQFCSPHDFFTLI 507
R E Q + + I EL+ H+A + +
Sbjct: 519 TGQHTWRFGLTRMLLGYAMESAQGEWQ-SVLPYDESSGLIAELVGHLASLLMQLNIWRRG 577
Query: 508 LGAKKGRQQFISRFGN-----------------EVIDVLDEFLNFTLRNEQNSYSSLQEL 550
L ++ ++++ + + + L + L L
Sbjct: 578 LAQERPLEEWLPVCRDMLNAFFLPDAETEAAMTLIEQQWQAIIAEGLGAQYGDAVPLSLL 637
Query: 551 ISELEQYPPTIKRAHSANHNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIKKMHIMP 610
EL Q + + V I T+ + + VV L+ V+ + +
Sbjct: 638 RDELAQRLDQERISQRFLAGPVNICTLMPMRSIPFKVVCLLGMNDGVYPRQLAPLGFDLM 697
Query: 611 SLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLIICKHSNT 670
S G S +++ L + A +L I +
Sbjct: 698 SQKPKRGDR----------------------SRRDDDRYLFLEALISAQQKLYISYIGRS 735
Query: 671 SNEKK 675
+
Sbjct: 736 IQDNS 740
Score = 29.4 bits (65), Expect = 3.9
Identities = 12/128 (9%), Positives = 36/128 (28%), Gaps = 4/128 (3%)
Query: 452 DIFKICTQRHETETVYEYIQKFANCGISKFQHVIKYIHELIHIAQFCSPH--DFFTLILG 509
D + + ++ + ++ + + Q I + L
Sbjct: 309 DYIYLLSDLESSQELDAFVDVTPDNLLHNIQSDILELENRAVAGVNIEEFSRSDNKRPLD 368
Query: 510 AKKGRQQFISRFG--NEVIDVLDEFLNFTLRNEQNSYSSLQELISELEQYPPTIKRAHSA 567
F EV + D L + + + ++++++ Y P I+ +
Sbjct: 369 PLDSSITFHVCHSPQREVEVLHDRLLAMLEEDPTLTPRDIIVMVADIDSYSPFIQAVFGS 428
Query: 568 NHNEVRIM 575
+ +
Sbjct: 429 APADRYLP 436
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl
reductase, beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 33.6 bits (76), Expect = 0.20
Identities = 32/155 (20%), Positives = 62/155 (40%), Gaps = 26/155 (16%)
Query: 157 NDLLKKRDVSAWIRYKIDQEINHILIDEVQDTSLIQWEVIRSLTEDFFVGKNTHSSPRTL 216
N LK R + W+ K + ++ + +TS+++ IR + + F G N
Sbjct: 865 NGNLKGRPYTGWVDSKTKEPVDDKDVKAKYETSILEHSGIRLIEPELFNGYNPEKK---- 920
Query: 217 FAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFSIIELPLSFRSTADIL---TV 273
+ Q + EP +E ++ G K I E+P + + +L T+
Sbjct: 921 ----EMIQEVIVEEDLEPFEASKETA--EQFKHQHGDKVDIFEIPETGEYSVKLLKGATL 974
Query: 274 -------VDKVFS--IPE--NAQ--GLSEDSTTTI 295
D++ + IP NA+ G+S+D + +
Sbjct: 975 YIPKALRFDRLVAGQIPTGWNAKTYGISDDIISQV 1009
Score = 28.6 bits (63), Expect = 5.9
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 23/75 (30%)
Query: 470 IQKFANCGISKFQHVIKYIHELIHIAQF--CSPHDFFTLILGAKKG-----RQQFISRFG 522
++ F GI+ + KY +H+++ CS G+ G R F RF
Sbjct: 1021 VEAFIASGITDPYEMYKY----VHVSEVGNCS---------GSGMGGVSALRGMFKDRFK 1067
Query: 523 NEVI--DVLDE-FLN 534
+E + D+L E F+N
Sbjct: 1068 DEPVQNDILQESFIN 1082
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD,
hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A*
2gk7_A
Length = 624
Score = 33.5 bits (75), Expect = 0.22
Identities = 29/134 (21%), Positives = 43/134 (32%), Gaps = 45/134 (33%)
Query: 552 SELEQYPPTIKRAHSANHNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIKKMHIMPS 611
S L QY H+ + EV I +V +G E + L S V +++H +
Sbjct: 511 SYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIIL----SCVRANEH----QGIGF 562
Query: 612 LNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLIICKHSNTS 671
LND R L V +TRA +II +
Sbjct: 563 LNDP---------------------------------RRLNVALTRARYGVIIVGNPKAL 589
Query: 672 NEKKSNQRTWYDMV 685
S Q W ++
Sbjct: 590 ----SKQPLWNHLL 599
>3dmn_A Putative DNA helicase; APC89291.2, lactobacillus plantarum WCFS1,
structural genomics, PSI-2, midwest center for
structural genomics; HET: MSE; 1.66A {Lactobacillus
plantarum}
Length = 174
Score = 31.9 bits (71), Expect = 0.63
Identities = 8/54 (14%), Positives = 21/54 (38%)
Query: 556 QYPPTIKRAHSANHNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIKKMHIM 609
+ I+ + V ++ AKGLE V + + + + + +++
Sbjct: 86 EQVTLIQTENQRLAPGVIVVPSFLAKGLEFDAVIVWNANQENYQREDERQLLYT 139
>2wjy_A Regulator of nonsense transcripts 1; alternative splicing, nonsense
mediated decay, zinc-finger, ATP-binding, polymorphism,
metal-binding, UPF2; 2.50A {Homo sapiens} PDB: 2wjv_A
2iyk_A
Length = 800
Score = 32.1 bits (72), Expect = 0.66
Identities = 29/134 (21%), Positives = 43/134 (32%), Gaps = 45/134 (33%)
Query: 552 SELEQYPPTIKRAHSANHNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIKKMHIMPS 611
S L QY H+ + EV I +V +G E + L S V +++H +
Sbjct: 687 SYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIIL----SCVRANEH----QGIGF 738
Query: 612 LNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLIICKHSNTS 671
LND R L V +TRA +II +
Sbjct: 739 LNDP---------------------------------RRLNVALTRARYGVIIVGNPKAL 765
Query: 672 NEKKSNQRTWYDMV 685
S Q W ++
Sbjct: 766 ----SKQPLWNHLL 775
>3hhm_A Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit
alpha isoform; PI3KCA, PI3K, PIK3R1,
phosphatidilynositol 3,4,5- triphosphate, wortmannin,
H1047R, ATP-binding, disease mutation, kinase; HET: KWT;
2.80A {Homo sapiens} PDB: 3hiz_A 2rd0_A 2enq_A
Length = 1091
Score = 30.7 bits (69), Expect = 1.7
Identities = 17/121 (14%), Positives = 36/121 (29%), Gaps = 7/121 (5%)
Query: 440 MLKSPLFNFSEDDIFKICTQRHETETVYEYIQKFANCGISKFQHVIKYIHELIHIAQFCS 499
+ PL +E + + + RH T+ E + K + + ++ L+
Sbjct: 558 STRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIK 617
Query: 500 PHDFFTLILGA---KKGRQQFISRFGNEVIDVLDEFLNF----TLRNEQNSYSSLQELIS 552
P L+ R + + D L+ EQ + L +
Sbjct: 618 PEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLL 677
Query: 553 E 553
+
Sbjct: 678 K 678
>3fg7_A Villin-1; actin binding protein, gelsolin, actin capping,
actin-binding, calcium, cytoplasm, cytoskeleton,
structural protein; 2.00A {Homo sapiens}
Length = 398
Score = 30.8 bits (69), Expect = 1.7
Identities = 20/85 (23%), Positives = 31/85 (36%), Gaps = 2/85 (2%)
Query: 516 QFISRFGNEVIDVLDEFLNF-TLRNEQNSYSSLQELISELEQYPPTIKRAHSANHNEVRI 574
ISR +V+ E NF + Y++ + L E P + + +
Sbjct: 239 DTISRTEKQVVVEGQEPANFWMALGGKAPYANTKRLQEENLVITPRLFECSNKTGRFLAT 298
Query: 575 MTVHTAKG-LESPVVFLVDTGSQVF 598
+ LE VFL+D QVF
Sbjct: 299 EIPDFNQDDLEEDDVFLLDVWDQVF 323
>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein,
ATP-binding, nucleotide-binding, hydrolase; 2.20A
{Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*
Length = 574
Score = 30.6 bits (68), Expect = 1.7
Identities = 6/17 (35%), Positives = 9/17 (52%)
Query: 649 RLLYVGMTRASDQLIIC 665
L+Y +TRA D+
Sbjct: 522 NLVYTALTRARDRFFSA 538
>3few_X Colicin S4; cell lysis, Y-RAY, cell killing, immune system; 2.45A
{Escherichia coli}
Length = 505
Score = 28.8 bits (64), Expect = 5.1
Identities = 12/129 (9%), Positives = 34/129 (26%), Gaps = 6/129 (4%)
Query: 81 QKNIITQEINKKSPDLKEKLKKSQDEFIK-----IRDRFNTYKMFKSTLASLTLAKYLNA 135
K I ++IN K+P+ + + + + + + + +
Sbjct: 164 AKAGIMEKINHKTPEEIYEALGFNKDESQRQEKAKQQAEDAWDRLPPNVRKFDVDVEQFH 223
Query: 136 HYEEAKKKNCVLDFE-DLIINTNDLLKKRDVSAWIRYKIDQEINHILIDEVQDTSLIQWE 194
+ VL + K + E + + + Q +
Sbjct: 224 YLVVLDDYGNVLSVTRTGVRPYVGSEKAKAGIMDKVDHKTPEEIYEALGFNNEEPQRQNQ 283
Query: 195 VIRSLTEDF 203
++ + F
Sbjct: 284 AKKAAYDVF 292
>3elb_A Ethanolamine-phosphate cytidylyltransferase; kennedy pathway, CMP,
CTP, phosphoethanolamine, SGC, structural genomics
consortium; HET: C5P; 2.00A {Homo sapiens}
Length = 341
Score = 28.8 bits (64), Expect = 5.9
Identities = 15/100 (15%), Positives = 35/100 (35%), Gaps = 18/100 (18%)
Query: 670 TSNEKKSNQRTWY-DMVYDSFHND-----ERVKKI----KLTNSINKDEWIAYEWSTHHP 719
+ E + + Y +D FH E+V ++ + ++ D+ + + ++P
Sbjct: 190 SGKEPQPGETVIYVAGAFDLFHIGHVDFLEKVHRLAERPYIIAGLHFDQEVNHYKGKNYP 249
Query: 720 ENTPLEREETIKQL--------MDEQKIPKKLFSPIKNDI 751
ER ++ + +L S K D+
Sbjct: 250 IMNLHERTLSVLACRYVSEVVIGAPYAVTAELLSHFKVDL 289
>1zro_A Erythrocyte binding antigen region II; EBA-175, RII, DBL, invasion,
HOST, malaria, disease, glycophorin, glycan, sialic
acid; HET: SO4; 2.25A {Plasmodium falciparum} SCOP:
a.264.1.1 a.264.1.1 PDB: 1zrl_A*
Length = 602
Score = 28.9 bits (64), Expect = 6.1
Identities = 16/98 (16%), Positives = 35/98 (35%), Gaps = 14/98 (14%)
Query: 73 FLTQKFTPQKNIITQEINKKSPD---------LKEKLKKSQDEFIKIRDRFNTYK----- 118
+ K + + + K D KE + K ++E+ K ++ Y+
Sbjct: 493 YCQDKTKMIETLKVECKEKPCEDDNCKRKCNSYKEWISKKKEEYNKQAKQYQEYQKGNNY 552
Query: 119 MFKSTLASLTLAKYLNAHYEEAKKKNCVLDFEDLIINT 156
S S+ YL + E+ N +F++ + +
Sbjct: 553 KMYSEFKSIKPEVYLKKYSEKCSNLNFEDEFKEELHSD 590
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1
PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C*
2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3dxj_C* 3eql_C*
1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C 1l9z_C 1i6v_C*
Length = 1119
Score = 28.2 bits (62), Expect = 8.8
Identities = 24/180 (13%), Positives = 53/180 (29%), Gaps = 13/180 (7%)
Query: 371 IQAKDILVLVRKRKDTPLITFLTRFL--KNDYKISVVGNDRFILTDHLAIKDLMALGRFI 428
++ ++ + ++ PL+ L R L + +G + ++ LM F
Sbjct: 176 VEPNGVVSMKVNKRKFPLVLLL-RVLGYDQETLARELGAYGEL------VQGLMDESVFA 228
Query: 429 LSQEDDLSFVCMLKSPLFNFSEDDIFKICTQRHETETVYEYIQKFANCGISKFQHVIKYI 488
+ E+ L + L P D Y+ + G K + +
Sbjct: 229 MRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDLGEA----GRYKAEEKLGIR 284
Query: 489 HELIHIAQFCSPHDFFTLILGAKKGRQQFISRFGNEVIDVLDEFLNFTLRNEQNSYSSLQ 548
+A+F + L + + +D +D N +R +
Sbjct: 285 LSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQF 344
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.319 0.134 0.385
Gapped
Lambda K H
0.267 0.0450 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 7,915,164
Number of extensions: 371036
Number of successful extensions: 1150
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1126
Number of HSP's successfully gapped: 53
Length of query: 952
Length of database: 5,693,230
Length adjustment: 101
Effective length of query: 851
Effective length of database: 3,244,586
Effective search space: 2761142686
Effective search space used: 2761142686
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: 61 (28.0 bits)