BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 001127
(1148 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3PJR|A Chain A, Helicase Substrate Complex
pdb|1QHG|A Chain A, Structure Of Dna Helicase Mutant With Adpnp
pdb|1PJR|A Chain A, Structure Of Dna Helicase
Length = 724
Score = 218 bits (554), Expect = 2e-56, Method: Compositional matrix adjust.
Identities = 215/730 (29%), Positives = 331/730 (45%), Gaps = 124/730 (16%)
Query: 245 LQSLNDQQLEAACGDMSTPLLIVAGPGSGKG---------------ISPSNILAMTFTTA 289
L LN +Q EA PLLI+AG GSGK ++P NILA+TFT
Sbjct: 9 LAHLNKEQQEA-VRTTEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNK 67
Query: 290 AASEMRDRIGSIVGKATAKELTISTFHSFSLQLCRSHAEKLERTSEFLIYGHGQQRRAII 349
AA EMR+R+ S++G A A+++ ISTFHS +++ R +++ F I Q +
Sbjct: 68 AAREMRERVQSLLGGA-AEDVWISTFHSMCVRILRRDIDRIGINRNFSILDPTDQ----L 122
Query: 350 EAVRLLENEKILVVKRISTDMLTTDGHFGYMRASLFMMNAMLFFSMSSFKLCQYNKFERD 409
++ + EK + K+ R L ++A
Sbjct: 123 SVMKTILKEKNIDPKKFEP------------RTILGTISA-------------------- 150
Query: 410 GMDVAKASGKTPAEFRKIG----DEIGAAILENYNGILRSCNALDYHDLISCSVKLLSTF 465
AK P +F K +++ + + + Y L ++LD+ DLI +++L
Sbjct: 151 ----AKNELLPPEQFAKRASTYYEKVVSDVYQEYQQRLLRNHSLDFDDLIMTTIQLFDRV 206
Query: 466 PEVFQEYQDSWKAIIVDEFQDTSAMQYSLLQILASH-NRITIVGDDDQSIFSFNGADISG 524
P+V YQ ++ I +DE+QDT+ QY+L++ LA I VGD DQSI+ + GADI
Sbjct: 207 PDVLHYYQYKFQYIHIDEYQDTNRAQYTLVKKLAERFQNICAVGDADQSIYRWRGADIQN 266
Query: 525 FDSFRKDFLNYKEIRLTRNYRSTRCIVEAASSLIQHNVKRCQLKNVQTDNSHGSKIIIKE 584
SF +D+ N K I L +NYRST+ I++AA+ +I+HNV R + K + T+N G I+ E
Sbjct: 267 ILSFERDYPNAKVILLEQNYRSTKRILQAANEVIEHNVNR-KPKRIWTENPEGKPILYYE 325
Query: 585 CHNEDAQCAFIIDKILEHASNGPASICSYGSIAILYRRQVSGKVFQTAFRERKIPFNI-H 643
NE + F+ +I E G Y A+LYR +V + + IP+ I
Sbjct: 326 AMNEADEAQFVAGRIREAVERGER---RYRDFAVLYRTNAQSRVMEEMLLKANIPYQIVG 382
Query: 644 GVAFYRKKVVRAIIAMLRTTLPGCDDGPYRRVFKAFXXXXXXXXXRVIDHIDKISTIRKC 703
G+ FY +K ++ I+A LR DD R+ ID + + + +
Sbjct: 383 GLKFYDRKEIKDILAYLRVIANPDDDLSLLRIINV---PKRGIGASTIDKLVRYAADHEL 439
Query: 704 SFISAACDI------FGAKISGTFKRSQLTQGRKVLLTLEMISKLVRREPSISAVITSVA 757
S A ++ A + RSQL Q T +
Sbjct: 440 SLFEALGELEMIGLGAKAAGALAAFRSQLEQW------------------------TQLQ 475
Query: 758 NMVPQKYLLEQRAVVDFDGGK-LLNEDNDLRSVLQYLLADVTDFLSTKFTAAKEEGNVDQ 816
V L+E+ V+D G + +L + + + Q L ++ +FLS K NV
Sbjct: 476 EYVSVTELVEE--VLDKSGYREMLKAERTIEA--QSRLENLDEFLSV----TKHFENVSD 527
Query: 817 DKKGCINVLK--AFIDYISERETEHFRTQRHDNENSVTLTTIHQSKGLEWDIVFVAKANE 874
D K I L A I + E + T++ ++V L T+H +KGLE+ +VF+ E
Sbjct: 528 D-KSLIAFLTDLALISDLDELDG----TEQAAEGDAVMLMTLHAAKGLEFPVVFLIGMEE 582
Query: 875 TEIPLVHEFNGAVNEKGTSVEEERRLLYVAMTRARKKLFILYVMMD---ANWQLLQPSRF 931
P N ++ + +EEERRL YV +TRA ++L + M N Q+ PSRF
Sbjct: 583 GIFP----HNRSLEDD-DEMEEERRLAYVGITRAEEELVLTSAQMRTLFGNIQMDPPSRF 637
Query: 932 LKEIPHHLRE 941
L EIP HL E
Sbjct: 638 LNEIPAHLLE 647
>pdb|2IS1|A Chain A, Crystal Structure Of Uvrd-Dna-So4 Complex
pdb|2IS1|B Chain B, Crystal Structure Of Uvrd-Dna-So4 Complex
pdb|2IS2|A Chain A, Crystal Structure Of Uvrd-Dna Binary Complex
pdb|2IS2|B Chain B, Crystal Structure Of Uvrd-Dna Binary Complex
pdb|2IS4|A Chain A, Crystal Structure Of Uvrd-Dna-Adpnp Ternary Complex
pdb|2IS4|B Chain B, Crystal Structure Of Uvrd-Dna-Adpnp Ternary Complex
pdb|2IS6|A Chain A, Crystal Structure Of Uvrd-Dna-Adpmgf3 Ternary Complex
pdb|2IS6|B Chain B, Crystal Structure Of Uvrd-Dna-Adpmgf3 Ternary Complex
Length = 680
Score = 214 bits (546), Expect = 2e-55, Method: Compositional matrix adjust.
Identities = 193/719 (26%), Positives = 323/719 (44%), Gaps = 109/719 (15%)
Query: 242 SKYLQSLNDQQLEAACGDMSTPLLIVAGPGSGK---------------GISPSNILAMTF 286
S L SLND+Q EA S LL++AG GSGK SP +I+A+TF
Sbjct: 4 SYLLDSLNDKQREAVAAPRSN-LLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTF 62
Query: 287 TTAAASEMRDRIGSIVGKATAKELTISTFHSFSLQLCRSHAEKLERTSEFLIYGHGQQRR 346
T AA+EMR RIG ++G + + + TFH + +L R+H +F I
Sbjct: 63 TNKAAAEMRHRIGQLMGTSQGG-MWVGTFHGLAHRLLRAHHMDANLPQDFQI-------- 113
Query: 347 AIIEAVRLLENEKILVVKRISTDMLTTDGHFGYMRASLFMMNAMLFFSMSSFKLCQYNKF 406
L +++ ++KR+ M + + R +++ +N+
Sbjct: 114 -------LDSEDQLRLLKRLIKAMNLDEKQWP-PRQAMWYINSQ---------------- 149
Query: 407 ERDGMDVAKASGKTPAEFRKIGDEIGAAILENYNGILRSCN---ALDYHDLISCSVKLLS 463
K G P + G+ + + Y +C+ +D+ +L+ + +L
Sbjct: 150 --------KDEGLRPHHIQSYGNPVEQTWQKVYQAYQEACDRAGLVDFAELLLRAHELWL 201
Query: 464 TFPEVFQEYQDSWKAIIVDEFQDTSAMQYSLLQILASH-NRITIVGDDDQSIFSFNGADI 522
P + Q Y++ + I+VDEFQDT+ +QY+ +++LA ++ IVGDDDQSI+ + GA +
Sbjct: 202 NKPHILQHYRERFTNILVDEFQDTNNIQYAWIRLLAGDTGKVMIVGDDDQSIYGWRGAQV 261
Query: 523 SGFDSFRKDFLNYKEIRLTRNYRSTRCIVEAASSLIQHNVKRCQLKNVQTDNSHGSKIII 582
F DF + IRL +NYRST I+ AA++LI++N R K + TD + G I +
Sbjct: 262 ENIQRFLNDFPGAETIRLEQNYRSTSNILSAANALIENNNGRLG-KKLWTDGADGEPISL 320
Query: 583 KECHNEDAQCAFIIDKILEHASNGPASICSYGSIAILYRRQVSGKVFQTAFRERKIPFNI 642
NE + F++++I NG A AILYR +V + A + +P+ I
Sbjct: 321 YCAFNELDEARFVVNRIKTWQDNGGA----LAECAILYRSNAQSRVLEEALLQASMPYRI 376
Query: 643 H-GVAFYRKKVVRAIIAMLRTTLPGCDDGPYRRVFKAFXXXXXXXXXRVIDHIDKISTIR 701
+ G+ F+ ++ ++ ++ LR + DD + RV R +D + + S R
Sbjct: 377 YGGMRFFERQEIKDALSYLRLIVNRNDDAAFERVVNT---PTRGIGDRTLDVVRQTSRDR 433
Query: 702 KCSFISAACDIFGAKISGTFKRSQLTQGRKVLLTLEMISKLVRREPSISAVITSVANMVP 761
+ + A ++ K L S L R I A+ A+M
Sbjct: 434 QLTLWQACRELLQEKA----------------LAGRAASALQRFMELIDALAQETADMP- 476
Query: 762 QKYLLEQRAVVDFDGGKLLNEDNDLRSVLQYLLADVTDFLS-TKFTAAKEEGNVDQDKKG 820
L Q V D G + + Q + ++ + ++ T+ + EE D+D
Sbjct: 477 ---LHVQTDRVIKDSGLRTMYEQEKGEKGQTRIENLEELVTATRQFSYNEE---DED--- 527
Query: 821 CINVLKAFIDYISERETEHFRTQRHDNENSVTLTTIHQSKGLEWDIVFVAKANETEIPLV 880
+ L+AF+ + + E Q +++V L T+H +KGLE+ VF+ E P
Sbjct: 528 -LMPLQAFLSHAA---LEAGEGQADTWQDAVQLMTLHSAKGLEFPQVFIVGMEEGMFPSQ 583
Query: 881 HEFNGAVNEKGTSVEEERRLLYVAMTRARKKLFILYV---MMDANWQLLQPSRFLKEIP 936
+ +G +EEERRL YV +TRA +KL + Y + +PSRF+ E+P
Sbjct: 584 MSLD-----EGGRLEEERRLAYVGVTRAMQKLTLTYAETRRLYGKEVYHRPSRFIGELP 637
>pdb|3LFU|A Chain A, Crystal Structure Of E. Coli Uvrd
Length = 647
Score = 213 bits (543), Expect = 4e-55, Method: Compositional matrix adjust.
Identities = 193/719 (26%), Positives = 322/719 (44%), Gaps = 109/719 (15%)
Query: 242 SKYLQSLNDQQLEAACGDMSTPLLIVAGPGSGK---------------GISPSNILAMTF 286
S L SLND+Q EA S LL++AG GSGK SP +I+A+TF
Sbjct: 4 SYLLDSLNDKQREAVAAPRSN-LLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTF 62
Query: 287 TTAAASEMRDRIGSIVGKATAKELTISTFHSFSLQLCRSHAEKLERTSEFLIYGHGQQRR 346
T AA+EMR RIG ++G + + + TFH + +L R+H +F I
Sbjct: 63 TNKAAAEMRHRIGQLMGTSQGG-MWVGTFHGLAHRLLRAHHMDANLPQDFQI-------- 113
Query: 347 AIIEAVRLLENEKILVVKRISTDMLTTDGHFGYMRASLFMMNAMLFFSMSSFKLCQYNKF 406
L +++ ++KR+ M + + R +++ +N+
Sbjct: 114 -------LDSEDQLRLLKRLIKAMNLDEKQWP-PRQAMWYINSQ---------------- 149
Query: 407 ERDGMDVAKASGKTPAEFRKIGDEIGAAILENYNGILRSCN---ALDYHDLISCSVKLLS 463
K G P + G+ + + Y +C+ +D+ +L+ + +L
Sbjct: 150 --------KDEGLRPHHIQSYGNPVEQTWQKVYQAYQEACDRAGLVDFAELLLRAHELWL 201
Query: 464 TFPEVFQEYQDSWKAIIVDEFQDTSAMQYSLLQILASH-NRITIVGDDDQSIFSFNGADI 522
P + Q Y++ + I+VDEFQDT+ +QY+ +++LA ++ IVGDDDQSI+ + GA +
Sbjct: 202 NKPHILQHYRERFTNILVDEFQDTNNIQYAWIRLLAGDTGKVMIVGDDDQSIYGWRGAQV 261
Query: 523 SGFDSFRKDFLNYKEIRLTRNYRSTRCIVEAASSLIQHNVKRCQLKNVQTDNSHGSKIII 582
F DF + IRL +NYRST I+ AA++LI++N R K + TD + G I +
Sbjct: 262 ENIQRFLNDFPGAETIRLEQNYRSTSNILSAANALIENNNGRLG-KKLWTDGADGEPISL 320
Query: 583 KECHNEDAQCAFIIDKILEHASNGPASICSYGSIAILYRRQVSGKVFQTAFRERKIPFNI 642
NE + F++++I NG A AILYR +V + A + +P+ I
Sbjct: 321 YCAFNELDEARFVVNRIKTWQDNGGA----LAECAILYRSNAQSRVLEEALLQASMPYRI 376
Query: 643 H-GVAFYRKKVVRAIIAMLRTTLPGCDDGPYRRVFKAFXXXXXXXXXRVIDHIDKISTIR 701
+ G+ F+ ++ ++ ++ LR DD + RV R +D + + S R
Sbjct: 377 YGGMRFFERQEIKDALSYLRLIANRNDDAAFERVVNT---PTRGIGDRTLDVVRQTSRDR 433
Query: 702 KCSFISAACDIFGAKISGTFKRSQLTQGRKVLLTLEMISKLVRREPSISAVITSVANMVP 761
+ + A ++ K L S L R I A+ A+M
Sbjct: 434 QLTLWQACRELLQEKA----------------LAGRAASALQRFMELIDALAQETADMP- 476
Query: 762 QKYLLEQRAVVDFDGGKLLNEDNDLRSVLQYLLADVTDFLS-TKFTAAKEEGNVDQDKKG 820
L Q V D G + + Q + ++ + ++ T+ + EE D+D
Sbjct: 477 ---LHVQTDRVIKDSGLRTMYEQEKGEKGQTRIENLEELVTATRQFSYNEE---DED--- 527
Query: 821 CINVLKAFIDYISERETEHFRTQRHDNENSVTLTTIHQSKGLEWDIVFVAKANETEIPLV 880
+ L+AF+ + + E Q +++V L T+H +KGLE+ VF+ E P
Sbjct: 528 -LMPLQAFLSHAA---LEAGEGQADTWQDAVQLMTLHSAKGLEFPQVFIVGMEEGMFPSQ 583
Query: 881 HEFNGAVNEKGTSVEEERRLLYVAMTRARKKLFILYV---MMDANWQLLQPSRFLKEIP 936
+ +G +EEERRL YV +TRA +KL + Y + +PSRF+ E+P
Sbjct: 584 MSLD-----EGGRLEEERRLAYVGVTRAMQKLTLTYAETRRLYGKEVYHRPSRFIGELP 637
>pdb|1UAA|A Chain A, E. Coli Rep HelicaseDNA COMPLEX
pdb|1UAA|B Chain B, E. Coli Rep HelicaseDNA COMPLEX
Length = 673
Score = 203 bits (516), Expect = 6e-52, Method: Compositional matrix adjust.
Identities = 195/726 (26%), Positives = 333/726 (45%), Gaps = 102/726 (14%)
Query: 260 MSTPLLIVAGPGSGK---------------GISPSNILAMTFTTAAASEMRDRIGSIVGK 304
++ P L++AG GSGK G +I A+TFT AA EM++R+G +G+
Sbjct: 14 VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLGR 73
Query: 305 ATAKELTISTFHSFSLQLCRSHAEKLERTSEFLIYGHGQQRRAIIEAVR-LLENEKILVV 363
A+ L ISTFH+ L + + L + F ++ Q + E L+E++K+L+
Sbjct: 74 KEARGLMISTFHTLGLDIIKREYAALGMKANFSLFDDTDQLALLKELTEGLIEDDKVLLQ 133
Query: 364 KRISTDMLTTDGHFGYMRASLFMMNAMLFFSMSSFKLCQYNKFERDGMDVAKASGKTPAE 423
+ IST +S++K N + A A G+
Sbjct: 134 QLIST--------------------------ISNWK----NDLKTPSQAAASAIGER--- 160
Query: 424 FRKIGDEIGAAILENYNGILRSCNALDYHDLISCSVKLLSTFPEVFQEYQDSWKAIIVDE 483
D I A Y+ L++CN LD+ DLI LL EV + +Q+ + ++VDE
Sbjct: 161 -----DRIFAHCYGLYDAHLKACNVLDFDDLILLPTLLLQANEEVRKRWQNKIRYLLVDE 215
Query: 484 FQDTSAMQYSLLQIL-ASHNRITIVGDDDQSIFSFNGADISGFDSFRKDFLNYKEIRLTR 542
+QDT+ QY L+++L S R T+VGDDDQSI+S+ GA +DF K I+L +
Sbjct: 216 YQDTNTSQYELVKLLVGSRARFTVVGDDDQSIYSWRGARPQNLVLLSQDFPALKVIKLEQ 275
Query: 543 NYRSTRCIVEAASSLIQHNVKRCQLKNVQTDNSHGSKIIIKECHNEDAQCAFIIDKILEH 602
NYRS+ I++AA+ LI +N + K + ++ +G+++ + +NE+ + + +++ H
Sbjct: 276 NYRSSGRILKAANILIANNPHVFE-KRLFSELGYGAELKVLSANNEEHEAERVTGELIAH 334
Query: 603 ASNGPASICSYGSIAILYRRQVSGKVFQTAFRERKIPFNIH-GVAFYRKKVVRAIIAMLR 661
+ Y AILYR +VF+ + +IP+ I G +F+ + ++ ++A LR
Sbjct: 335 HF---VNKTQYKDYAILYRGNHQSRVFEKFLMQNRIPYKISGGTSFFSRPEIKDLLAYLR 391
Query: 662 TTLPGCDDGPYRRVFKAFXXXXXXXXXRVIDHIDKISTIRKCSFISAACDIFGAKISGTF 721
DD + R+ + + + + R S +A+ D+ +S T
Sbjct: 392 VLTNPDDDSAFLRIVNT---PKREIGPATLKKLGEWAMTRNKSMFTASFDM---GLSQTL 445
Query: 722 KRSQLTQGRKVLLTLEMISKLVRREPSISAVITSVANMVPQKYLLEQRAVVDFDGGKLLN 781
+ L I +L REP I+AV + M + +L E ++ N
Sbjct: 446 SGRGYEALTRFTHWLAEIQRLAEREP-IAAVRDLIHGMDYESWLYETSPSPKAAEMRMKN 504
Query: 782 EDNDLRSVLQYLLADVTDFLSTKFTAAKEEGNVDQDKKGCINVLKAFI--DYISERETEH 839
+ L + +T+ L EG+ + V+ F D + E+E
Sbjct: 505 --------VNQLFSWMTEML---------EGSELDEPMTLTQVVTRFTLRDMMERGESE- 546
Query: 840 FRTQRHDNENSVTLTTIHQSKGLEWDIVFVAKANETEIPLVHEFNGAVNEKGTSVEEERR 899
+ + V L T+H SKGLE+ V++ E +P H+ +++E +++EERR
Sbjct: 547 ------EELDQVQLMTLHASKGLEFPYVYMVGMEEGFLP--HQ--SSIDED--NIDEERR 594
Query: 900 LLYVAMTRARKKL-FILYVMMDANWQLL--QPSRFLKEIPHHLREVQAEQSVQDQHENIP 956
L YV +TRA+K+L F L +L+ +PSRFL E+P + E+ V E +
Sbjct: 595 LAYVGITRAQKELTFTLCKERRQYGELVRPEPSRFLLELPQDDLIWEQERKVVSAEERMQ 654
Query: 957 EGTAQF 962
+G +
Sbjct: 655 KGQSHL 660
>pdb|2PJR|A Chain A, Helicase Product Complex
pdb|2PJR|F Chain F, Helicase Product Complex
Length = 548
Score = 192 bits (489), Expect = 8e-49, Method: Compositional matrix adjust.
Identities = 142/452 (31%), Positives = 214/452 (47%), Gaps = 67/452 (14%)
Query: 245 LQSLNDQQLEAACGDMSTPLLIVAGPGSGKG---------------ISPSNILAMTFTTA 289
L LN +Q EA PLLI+AG GSGK ++P NILA+TFT
Sbjct: 9 LAHLNKEQQEA-VRTTEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNK 67
Query: 290 AASEMRDRIGSIVGKATAKELTISTFHSFSLQLCRSHAEKLERTSEFLIYGHGQQRRAII 349
AA EMR+R+ S++G A A+++ ISTFHS +++ R +++ F I Q +
Sbjct: 68 AAREMRERVQSLLGGA-AEDVWISTFHSMCVRILRRDIDRIGINRNFSILDPTDQLSVM- 125
Query: 350 EAVRLLENEKILVVKRISTDMLTTDGHFGYMRASLFMMNAMLFFSMSSFKLCQYNKFERD 409
+ IL K I G + A
Sbjct: 126 --------KTILKEKNIDPKKFEPRTILGTISA--------------------------- 150
Query: 410 GMDVAKASGKTPAEFRKIG----DEIGAAILENYNGILRSCNALDYHDLISCSVKLLSTF 465
AK P +F K +++ + + + Y L ++LD+ DLI +++L
Sbjct: 151 ----AKNELLPPEQFAKRASTYYEKVVSDVYQEYQQRLLRNHSLDFDDLIMTTIQLFDRV 206
Query: 466 PEVFQEYQDSWKAIIVDEFQDTSAMQYSLLQILASH-NRITIVGDDDQSIFSFNGADISG 524
P+V YQ ++ I +DE+QDT+ QY+L++ LA I VGD DQSI+ + GADI
Sbjct: 207 PDVLHYYQYKFQYIHIDEYQDTNRAQYTLVKKLAERFQNICAVGDADQSIYRWRGADIQN 266
Query: 525 FDSFRKDFLNYKEIRLTRNYRSTRCIVEAASSLIQHNVKRCQLKNVQTDNSHGSKIIIKE 584
SF +D+ N K I L +NYRST+ I++AA+ +I+HNV R + K + T+N G I+ E
Sbjct: 267 ILSFERDYPNAKVILLEQNYRSTKRILQAANEVIEHNVNR-KPKRIWTENPEGKPILYYE 325
Query: 585 CHNEDAQCAFIIDKILEHASNGPASICSYGSIAILYRRQVSGKVFQTAFRERKIPFNI-H 643
NE + F+ +I E G Y A+LYR +V + + IP+ I
Sbjct: 326 AMNEADEAQFVAGRIREAVERGER---RYRDFAVLYRTNAQSRVMEEMLLKANIPYQIVG 382
Query: 644 GVAFYRKKVVRAIIAMLRTTLPGCDDGPYRRV 675
G+ FY +K ++ I+A LR DD R+
Sbjct: 383 GLKFYDRKEIKDILAYLRVIANPDDDLSLLRI 414
>pdb|1QHH|B Chain B, Structure Of Dna Helicase With Adpnp
Length = 273
Score = 144 bits (362), Expect = 3e-34, Method: Composition-based stats.
Identities = 87/249 (34%), Positives = 137/249 (55%), Gaps = 6/249 (2%)
Query: 429 DEIGAAILENYNGILRSCNALDYHDLISCSVKLLSTFPEVFQEYQDSWKAIIVDEFQDTS 488
+++ + + + Y L ++LD+ DLI +++L P+V YQ ++ I +DE+QDT+
Sbjct: 3 EKVVSDVYQEYQQRLLRNHSLDFDDLIMTTIQLFDRVPDVLHYYQYKFQYIHIDEYQDTN 62
Query: 489 AMQYSLLQILASH-NRITIVGDDDQSIFSFNGADISGFDSFRKDFLNYKEIRLTRNYRST 547
QY+L++ LA I VGD DQSI+ + GADI SF +D+ N K I L +NYRST
Sbjct: 63 RAQYTLVKKLAERFQNICAVGDADQSIYRWRGADIQNILSFERDYPNAKVILLEQNYRST 122
Query: 548 RCIVEAASSLIQHNVKRCQLKNVQTDNSHGSKIIIKECHNEDAQCAFIIDKILEHASNGP 607
+ I++AA+ +I+HNV R + K + T+N G I+ E NE + F+ +I E G
Sbjct: 123 KRILQAANEVIEHNVNR-KPKRIWTENPEGKPILYYEAMNEADEAQFVAGRIREAVERGE 181
Query: 608 ASICSYGSIAILYRRQVSGKVFQTAFRERKIPFNI-HGVAFYRKKVVRAIIAMLRTTLPG 666
Y A+LYR +V + + IP+ I G+ FY +K ++ I+A LR
Sbjct: 182 R---RYRDFAVLYRTNAQSRVMEEMLLKANIPYQIVGGLKFYDRKEIKDILAYLRVIANP 238
Query: 667 CDDGPYRRV 675
DD R+
Sbjct: 239 DDDLSLLRI 247
>pdb|1QHH|A Chain A, Structure Of Dna Helicase With Adpnp
Length = 167
Score = 67.4 bits (163), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 43/111 (38%), Positives = 62/111 (55%), Gaps = 17/111 (15%)
Query: 243 KYLQSLNDQQLEAACGDMSTPLLIVAGPGSGKG---------------ISPSNILAMTFT 287
+ L LN +Q EA PLLI+AG GSGK ++P NILA+TFT
Sbjct: 7 QLLAHLNKEQQEA-VRTTEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFT 65
Query: 288 TAAASEMRDRIGSIVGKATAKELTISTFHSFSLQLCRSHAEKLERTSEFLI 338
AA EMR+R+ S++G A A+++ ISTFHS +++ R +++ F I
Sbjct: 66 NKAAREMRERVQSLLGGA-AEDVWISTFHSMCVRILRRDIDRIGINRNFSI 115
>pdb|1QHH|D Chain D, Structure Of Dna Helicase With Adpnp
Length = 169
Score = 56.6 bits (135), Expect = 8e-08, Method: Composition-based stats.
Identities = 38/101 (37%), Positives = 53/101 (52%), Gaps = 8/101 (7%)
Query: 849 NSVTLTTIHQSKGLEWDIVFVAKANETEIPLVHEFNGAVNEKGTSVEEERRLLYVAMTRA 908
++V L T+H +KGLE+ +VF+ E P +EEERRL YV +TRA
Sbjct: 2 DAVMLMTLHAAKGLEFPVVFLIGMEEGIFPHNRSLEDD-----DEMEEERRLAYVGITRA 56
Query: 909 RKKLFILYVMMD---ANWQLLQPSRFLKEIPHHLREVQAEQ 946
++L + M N Q+ PSRFL EIP HL E + +
Sbjct: 57 EEELVLTSAQMRTLFGNIQMDPPSRFLNEIPAHLLETASRR 97
>pdb|2PJR|B Chain B, Helicase Product Complex
pdb|2PJR|G Chain G, Helicase Product Complex
Length = 95
Score = 55.8 bits (133), Expect = 1e-07, Method: Composition-based stats.
Identities = 38/99 (38%), Positives = 52/99 (52%), Gaps = 8/99 (8%)
Query: 849 NSVTLTTIHQSKGLEWDIVFVAKANETEIPLVHEFNGAVNEKGTSVEEERRLLYVAMTRA 908
++V L T+H +KGLE+ +VF+ E P +EEERRL YV +TRA
Sbjct: 2 DAVMLMTLHAAKGLEFPVVFLIGMEEGIFPHNRSLEDD-----DEMEEERRLAYVGITRA 56
Query: 909 RKKLFILYVMMD---ANWQLLQPSRFLKEIPHHLREVQA 944
++L + M N Q+ PSRFL EIP HL E +
Sbjct: 57 EEELVLTSAQMRTLFGNIQMDPPSRFLNEIPAHLLETAS 95
>pdb|3U44|A Chain A, Crystal Structure Of Addab-Dna Complex
pdb|3U4Q|A Chain A, Structure Of Addab-Dna Complex At 2.8 Angstroms
Length = 1232
Score = 48.9 bits (115), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 34/98 (34%), Positives = 54/98 (55%), Gaps = 9/98 (9%)
Query: 472 YQDSWKAIIVDEFQDTSAMQYSLLQILASHNRIT----IVGDDDQSIFSFNGADISGFDS 527
YQ+ + ++VDE+QDT+ +Q S+LQ++ S T +VGD QSI+ F A+ F S
Sbjct: 397 YQEQFHEVLVDEYQDTNLVQESILQLVTSGPEETGNLFMVGDVKQSIYRFRLAEPLLFLS 456
Query: 528 FRKDFLNYKE-----IRLTRNYRSTRCIVEAASSLIQH 560
K F E I L +N+RS I+++ + L +
Sbjct: 457 KYKRFTESGEGTGRKIDLNKNFRSRADILDSTNFLFKQ 494
Score = 44.7 bits (104), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 44/147 (29%), Positives = 66/147 (44%), Gaps = 48/147 (32%)
Query: 819 KGCINVLKAFIDYISERETEHFRTQR--HDNENSVTLTTIHQSKGLEWDIVFVA------ 870
+G L+ FI+ + ER + T R + E+ V L TIH SKGLE+ +VFVA
Sbjct: 756 RGLFRFLR-FIERMQER-GDDLGTARGLSEQEDVVRLMTIHSSKGLEFPVVFVAGLGRNF 813
Query: 871 --------------------------KANETEIPLVHEFNGAVNEKGTS--VEEERRLLY 902
+ + +PL+ A+ +K + EE R+LY
Sbjct: 814 NMMDLNKSYLLDKELGFGTKYIHPQLRISYPTLPLI-----AMKKKMRRELLSEELRVLY 868
Query: 903 VAMTRARKKLFILYVMMD-----ANWQ 924
VA+TRA++KLF++ D A WQ
Sbjct: 869 VALTRAKEKLFLIGSCKDHQKQLAKWQ 895
Score = 36.2 bits (82), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 39/95 (41%), Gaps = 32/95 (33%)
Query: 264 LLIVAGPGSGKG-----------------ISPSNILAMTFTTAAASEMRDRIGSIVGKAT 306
+L+ A GSGK I +L +TFT A+A+EM+ RI + K
Sbjct: 26 ILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAEALEKEL 85
Query: 307 AK---------------ELTISTFHSFSLQLCRSH 326
+ +IST HSF LQ+ + +
Sbjct: 86 VQRPGSLHIRRQLSLLNRASISTLHSFCLQVLKKY 120
>pdb|1W36|B Chain B, Recbcd:dna Complex
pdb|1W36|E Chain E, Recbcd:dna Complex
pdb|3K70|B Chain B, Crystal Structure Of The Complete Initiation Complex Of
Recbcd
pdb|3K70|E Chain E, Crystal Structure Of The Complete Initiation Complex Of
Recbcd
Length = 1180
Score = 47.4 bits (111), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 43/82 (52%), Gaps = 5/82 (6%)
Query: 480 IVDEFQDTSAMQYSLLQILASH---NRITIVGDDDQSIFSFNGADISGFDSFRKDFLNYK 536
++DEFQDT QY + + + H + ++GD Q+I++F GADI + R + +
Sbjct: 382 MIDEFQDTDPQQYRIFRRIWHHQPETALLLIGDPKQAIYAFRGADIFTYMKARSEV--HA 439
Query: 537 EIRLTRNYRSTRCIVEAASSLI 558
L N+RS +V + + L
Sbjct: 440 HYTLDTNWRSAPGMVNSVNKLF 461
Score = 32.3 bits (72), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 38/78 (48%), Gaps = 16/78 (20%)
Query: 847 NENSVTLTTIHQSKGLEWDIV---FVAKANETEIPLVHEFNG--------AVNEKGTSVE 895
+++ V + TIH+SKGLE+ +V F+ E H+ + A E E
Sbjct: 732 DKHLVQIVTIHKSKGLEYPLVWLPFITNFRVQEQAFYHDRHSFEAVLDLNAAPESVDLAE 791
Query: 896 EER-----RLLYVAMTRA 908
ER RLLYVA+TR+
Sbjct: 792 AERLAEDLRLLYVALTRS 809
>pdb|3E1S|A Chain A, Structure Of An N-Terminal Truncation Of Deinococcus
Radiodurans Recd2
pdb|3GP8|A Chain A, Crystal Structure Of The Binary Complex Of Recd2 With Dna
pdb|3GPL|A Chain A, Crystal Structure Of The Ternary Complex Of Recd2 With Dna
And Adpnp
pdb|3GPL|B Chain B, Crystal Structure Of The Ternary Complex Of Recd2 With Dna
And Adpnp
Length = 574
Score = 32.3 bits (72), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 17/59 (28%)
Query: 855 TIHQSKGLEWDIVFVAKANETEIPLVHEFNGAVNEKGTSVEEERRLLYVAMTRARKKLF 913
T+H+++G EW V +E +P++ R L+Y A+TRAR + F
Sbjct: 495 TVHRAQGSEWGTVL-GVLHEAHMPML----------------SRNLVYTALTRARDRFF 536
>pdb|1SZQ|A Chain A, Crystal Structure Of 2-Methylcitrate Dehydratase
pdb|1SZQ|B Chain B, Crystal Structure Of 2-Methylcitrate Dehydratase
Length = 483
Score = 31.2 bits (69), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 40/140 (28%), Positives = 62/140 (44%), Gaps = 19/140 (13%)
Query: 780 LNEDNDLRSVLQYLLADVTDFLSTKFTAAKEEGNVDQDKKGCINVLKAFIDYISERETEH 839
LN D +QY +A L + TAA E NV QDK+ + A + I+ E
Sbjct: 338 LNNPADRDHCIQYXVA--IPLLFGRLTAADYEDNVAQDKR-----IDALREKINCFEDPA 390
Query: 840 FRTQRHDNENS--VTLTTIHQSKGLEWDIVFV------AKANETEIP-LVHEFNGAVN-E 889
F HD E T+ + G ++ V V A+ + IP LV +F +N
Sbjct: 391 FTADYHDPEKRAIANAITLEFTDGTRFEEVVVEYPIGHARRRQDGIPKLVDKFK--INLA 448
Query: 890 KGTSVEEERRLLYVAMTRAR 909
+ +++R+L V++ RAR
Sbjct: 449 RQFPTRQQQRILEVSLDRAR 468
>pdb|1JK9|B Chain B, Heterodimer Between H48f-Ysod1 And Yccs
pdb|1JK9|D Chain D, Heterodimer Between H48f-Ysod1 And Yccs
Length = 249
Score = 30.8 bits (68), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 593 AFIIDKILEHASNGPASICSYGSIAILYR--------RQVSGKVFQTAFRERK 637
+F+I K L H N P+S+ Y + ++ R +QV +T + ERK
Sbjct: 189 SFVISKSLNHPENEPSSVKDYSFLGVIARSAGVWENNKQVCACTGKTVWEERK 241
>pdb|4IF8|A Chain A, Structure Of Vaspin
pdb|4IF8|B Chain B, Structure Of Vaspin
Length = 414
Score = 29.6 bits (65), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 151 DFDDSILQEIDAICEKSAAKDVRKAQNSGIYEETHQNDNSCTHL 194
+FD ++ +E D EK+++ V SGIY+ + + SCT L
Sbjct: 217 EFDPNVTKEEDFFLEKNSSVKVPMMFRSGIYQVGYDDKLSCTIL 260
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.133 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 31,049,706
Number of Sequences: 62578
Number of extensions: 1222983
Number of successful extensions: 3081
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 3010
Number of HSP's gapped (non-prelim): 35
length of query: 1148
length of database: 14,973,337
effective HSP length: 109
effective length of query: 1039
effective length of database: 8,152,335
effective search space: 8470276065
effective search space used: 8470276065
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)