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= 001046
(1176 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3KX2|B Chain B, Crystal Structure Of Prp43p In Complex With Adp
pdb|3KX2|A Chain A, Crystal Structure Of Prp43p In Complex With Adp
Length = 767
Score = 676 bits (1744), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 352/733 (48%), Positives = 494/733 (67%), Gaps = 33/733 (4%)
Query: 460 IPKDLNRPWEDPMPETGERHLAQELRGVGLSAYDMPEWKKDAFGKALTFGQRS----KLS 515
I ++L++ P E H A E +G+ E +K GK F R +
Sbjct: 26 IAEELSKQHPLPSEEPLVHHDAGEFKGLQRHHTSAEEAQKLEDGKINPFTGREFTPKYVD 85
Query: 516 IQEQRQSLPIYKLKKELIQAVHDNQVLVVIGETGSGKTTQVTQYLA--EAGYTTRGKIGC 573
I + R+ LP++ + E ++ +NQ++V +GETGSGKTTQ+ Q++ E + ++ C
Sbjct: 86 ILKIRRELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVAC 145
Query: 574 TQPRRVAAMSVAKRVAEEFGCRLGEEVGYAIRFEDCTGPDTVIKYMTDGMLLREILIDDN 633
TQPRRVAAMSVA+RVAEE +LGEEVGY+IRFE+ T T++KYMTDGMLLRE + D +
Sbjct: 146 TQPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFENKTSNKTILKYMTDGMLLREAMEDHD 205
Query: 634 LSQYSVIMLDEAHERTIHTDVLFGLLKQLVKRRPDLRLIVTSATLDAEKFSGYFFNCNIF 693
LS+YS I+LDEAHERT+ TD+L GLLKQ+VKRRPDL++I+ SATLDAEKF YF + +
Sbjct: 206 LSRYSCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSATLDAEKFQRYFNDAPLL 265
Query: 694 TIPGRTFPVEILYTKQPESDYLDASLITVLQIHLTEPEGDILLFLTGQEEIDFACQSL-- 751
+PGRT+PVE+ YT + + DYLD+++ TVLQIH TE GDILLFLTG++EI+ A + +
Sbjct: 266 AVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILLFLTGEDEIEDAVRKISL 325
Query: 752 ----YERMKGLGKNVPELIILPVYSALPSEMQSRIFDPAP------PGKRKVVVATNIAE 801
R +G G L + P+Y +LP Q RIF+PAP PG RKVV++TNIAE
Sbjct: 326 EGDQLVREEGCGP----LSVYPLYGSLPPHQQQRIFEPAPESHNGRPG-RKVVISTNIAE 380
Query: 802 ASLTIDGIFYVIDPGFAKQNVYNPKQGLDSLVITPISQASAKQRAGRAGRTGPGKCYRLY 861
SLTIDGI YV+DPGF+KQ VYNP+ ++SL+++PIS+ASA+QRAGRAGRT PGKC+RLY
Sbjct: 381 TSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRTRPGKCFRLY 440
Query: 862 TESAYRNEMSPTSIPEIQRINLGFTTLTMKAMGINDLLSFDFMDPPSPQALISAMEQLYS 921
TE A++ E+ S PEI R NL T L +K +GI+DL+ FDFMDPP+P+ ++ A+E+L
Sbjct: 441 TEEAFQKELIEQSYPEILRSNLSSTVLELKKLGIDDLVHFDFMDPPAPETMMRALEELNY 500
Query: 922 LGALDEEGLLTKLGRKMAEFPLDPPLSKMLLASVDLGCSDEILTIIAMIQTGNIFYRPRE 981
L LD+EG LT LGR ++FPLDP L+ ML+ S + CS EILTI+AM+ N+F RP +
Sbjct: 501 LACLDDEGNLTPLGRLASQFPLDPMLAVMLIGSFEFQCSQEILTIVAMLSVPNVFIRPTK 560
Query: 982 KQAQADQKRAKFFQPEGDHLTLLAVYEAWKAKNFS----GPWCFENFVQSRSLRRAQDVR 1037
+ +AD + F P+GDH+TLL VY A+K+ WC ++++ RSL A ++R
Sbjct: 561 DKKRADDAKNIFAHPDGDHITLLNVYHAFKSDEAYEYGIHKWCRDHYLNYRSLSAADNIR 620
Query: 1038 KQLLSIMDKYKLDVMS----AGKNFTKIRKAITAGFFFHAARK-DPQEGYRTLVENQPVY 1092
QL +M++Y L++ + + K F IRKA+ +GFF A+K +GY T+ +NQ V
Sbjct: 621 SQLERLMNRYNLELNTTDYESPKYFDNIRKALASGFFMQVAKKRSGAKGYITVKDNQDVL 680
Query: 1093 IHPSSALFQRQPDWVIYHELVMTTKEYMREVTVIDPKWLVDLAPRFFKVADPTKMSKRKR 1152
IHPS+ L +WVIY+E V+T+K Y+R VT + P+WL+++AP ++ +++ K +
Sbjct: 681 IHPSTVL-GHDAEWVIYNEFVLTSKNYIRTVTSVRPEWLIEIAPAYYDLSNFQKGDVKLS 739
Query: 1153 QERIEPLYDRYHE 1165
ERI+ DR +E
Sbjct: 740 LERIKEKVDRLNE 752
>pdb|2XAU|A Chain A, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In
Complex With Adp
pdb|2XAU|B Chain B, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In
Complex With Adp
Length = 773
Score = 676 bits (1744), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 352/733 (48%), Positives = 494/733 (67%), Gaps = 33/733 (4%)
Query: 460 IPKDLNRPWEDPMPETGERHLAQELRGVGLSAYDMPEWKKDAFGKALTFGQRS----KLS 515
I ++L++ P E H A E +G+ E +K GK F R +
Sbjct: 26 IAEELSKQHPLPSEEPLVHHDAGEFKGLQRHHTSAEEAQKLEDGKINPFTGREFTPKYVD 85
Query: 516 IQEQRQSLPIYKLKKELIQAVHDNQVLVVIGETGSGKTTQVTQYLA--EAGYTTRGKIGC 573
I + R+ LP++ + E ++ +NQ++V +GETGSGKTTQ+ Q++ E + ++ C
Sbjct: 86 ILKIRRELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVAC 145
Query: 574 TQPRRVAAMSVAKRVAEEFGCRLGEEVGYAIRFEDCTGPDTVIKYMTDGMLLREILIDDN 633
TQPRRVAAMSVA+RVAEE +LGEEVGY+IRFE+ T T++KYMTDGMLLRE + D +
Sbjct: 146 TQPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFENKTSNKTILKYMTDGMLLREAMEDHD 205
Query: 634 LSQYSVIMLDEAHERTIHTDVLFGLLKQLVKRRPDLRLIVTSATLDAEKFSGYFFNCNIF 693
LS+YS I+LDEAHERT+ TD+L GLLKQ+VKRRPDL++I+ SATLDAEKF YF + +
Sbjct: 206 LSRYSCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSATLDAEKFQRYFNDAPLL 265
Query: 694 TIPGRTFPVEILYTKQPESDYLDASLITVLQIHLTEPEGDILLFLTGQEEIDFACQSL-- 751
+PGRT+PVE+ YT + + DYLD+++ TVLQIH TE GDILLFLTG++EI+ A + +
Sbjct: 266 AVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILLFLTGEDEIEDAVRKISL 325
Query: 752 ----YERMKGLGKNVPELIILPVYSALPSEMQSRIFDPAP------PGKRKVVVATNIAE 801
R +G G L + P+Y +LP Q RIF+PAP PG RKVV++TNIAE
Sbjct: 326 EGDQLVREEGCGP----LSVYPLYGSLPPHQQQRIFEPAPESHNGRPG-RKVVISTNIAE 380
Query: 802 ASLTIDGIFYVIDPGFAKQNVYNPKQGLDSLVITPISQASAKQRAGRAGRTGPGKCYRLY 861
SLTIDGI YV+DPGF+KQ VYNP+ ++SL+++PIS+ASA+QRAGRAGRT PGKC+RLY
Sbjct: 381 TSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRTRPGKCFRLY 440
Query: 862 TESAYRNEMSPTSIPEIQRINLGFTTLTMKAMGINDLLSFDFMDPPSPQALISAMEQLYS 921
TE A++ E+ S PEI R NL T L +K +GI+DL+ FDFMDPP+P+ ++ A+E+L
Sbjct: 441 TEEAFQKELIEQSYPEILRSNLSSTVLELKKLGIDDLVHFDFMDPPAPETMMRALEELNY 500
Query: 922 LGALDEEGLLTKLGRKMAEFPLDPPLSKMLLASVDLGCSDEILTIIAMIQTGNIFYRPRE 981
L LD+EG LT LGR ++FPLDP L+ ML+ S + CS EILTI+AM+ N+F RP +
Sbjct: 501 LACLDDEGNLTPLGRLASQFPLDPMLAVMLIGSFEFQCSQEILTIVAMLSVPNVFIRPTK 560
Query: 982 KQAQADQKRAKFFQPEGDHLTLLAVYEAWKAKNFS----GPWCFENFVQSRSLRRAQDVR 1037
+ +AD + F P+GDH+TLL VY A+K+ WC ++++ RSL A ++R
Sbjct: 561 DKKRADDAKNIFAHPDGDHITLLNVYHAFKSDEAYEYGIHKWCRDHYLNYRSLSAADNIR 620
Query: 1038 KQLLSIMDKYKLDVMS----AGKNFTKIRKAITAGFFFHAARK-DPQEGYRTLVENQPVY 1092
QL +M++Y L++ + + K F IRKA+ +GFF A+K +GY T+ +NQ V
Sbjct: 621 SQLERLMNRYNLELNTTDYESPKYFDNIRKALASGFFMQVAKKRSGAKGYITVKDNQDVL 680
Query: 1093 IHPSSALFQRQPDWVIYHELVMTTKEYMREVTVIDPKWLVDLAPRFFKVADPTKMSKRKR 1152
IHPS+ L +WVIY+E V+T+K Y+R VT + P+WL+++AP ++ +++ K +
Sbjct: 681 IHPSTVL-GHDAEWVIYNEFVLTSKNYIRTVTSVRPEWLIEIAPAYYDLSNFQKGDVKLS 739
Query: 1153 QERIEPLYDRYHE 1165
ERI+ DR +E
Sbjct: 740 LERIKEKVDRLNE 752
>pdb|3I4U|A Chain A, Crystal Structure Analysis Of A Helicase Associated Domain
Length = 270
Score = 370 bits (951), Expect = e-102, Method: Compositional matrix adjust.
Identities = 164/234 (70%), Positives = 205/234 (87%)
Query: 910 QALISAMEQLYSLGALDEEGLLTKLGRKMAEFPLDPPLSKMLLASVDLGCSDEILTIIAM 969
+ LI+AMEQLY+LGALD+EGLLT+LGR+MAEFPL+P L KML+ SV LGCS+E+LTI++M
Sbjct: 18 ETLITAMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSM 77
Query: 970 IQTGNIFYRPREKQAQADQKRAKFFQPEGDHLTLLAVYEAWKAKNFSGPWCFENFVQSRS 1029
+ N+FYRP++KQA ADQK+AKF Q EGDHLTLLAVY +WK FS PWC+ENF+Q+RS
Sbjct: 78 LSVQNVFYRPKDKQALADQKKAKFHQTEGDHLTLLAVYNSWKNNKFSNPWCYENFIQARS 137
Query: 1030 LRRAQDVRKQLLSIMDKYKLDVMSAGKNFTKIRKAITAGFFFHAARKDPQEGYRTLVENQ 1089
LRRAQD+RKQ+L IMD++KLDV+S GK+ +++KAI +GFF +AA+KDPQEGYRTL++ Q
Sbjct: 138 LRRAQDIRKQMLGIMDRHKLDVVSCGKSTVRVQKAICSGFFRNAAKKDPQEGYRTLIDQQ 197
Query: 1090 PVYIHPSSALFQRQPDWVIYHELVMTTKEYMREVTVIDPKWLVDLAPRFFKVAD 1143
VYIHPSSALF RQP+WV+YHELV+TTKEYMREVT IDP+WLV+ AP FFKV +
Sbjct: 198 VVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRWLVEFAPAFFKVLE 251
>pdb|3LLM|A Chain A, Crystal Structure Analysis Of A Rna Helicase
pdb|3LLM|B Chain B, Crystal Structure Analysis Of A Rna Helicase
Length = 235
Score = 135 bits (340), Expect = 1e-31, Method: Composition-based stats.
Identities = 72/186 (38%), Positives = 116/186 (62%), Gaps = 7/186 (3%)
Query: 515 SIQEQRQSLPIYKLKKELIQAVHDNQVLVVIGETGSGKTTQVTQYLAEAGYTTRGKIGC- 573
+I ++R+ LP+ K + E+++A+ N V+++ G TG GKTTQV Q++ + C
Sbjct: 52 AILQERELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECN 111
Query: 574 ---TQPRRVAAMSVAKRVAEEFGCRLGEEVGYAIRFEDCTG-PDTVIKYMTDGMLLREIL 629
TQPRR++A+SVA+RVA E G G+ GY++RFE P I + T G+LLR++
Sbjct: 112 IVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESILPRPHASIXFCTVGVLLRKL- 170
Query: 630 IDDNLSQYSVIMLDEAHERTIHTDVLFGLLKQLVKRRPDLRLIVTSATLDAEKFSGYFFN 689
+ + S +++DE HER I+TD L +L+ +V+ P++R+++ SAT+D F YFFN
Sbjct: 171 -EAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLXSATIDTSXFCEYFFN 229
Query: 690 CNIFTI 695
C I +
Sbjct: 230 CPIIEV 235
>pdb|2EQS|A Chain A, Solution Structure Of The S1 Rna Binding Domain Of Human
Atp-Dependent Rna Helicase Dhx8
Length = 103
Score = 88.6 bits (218), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 45/93 (48%), Positives = 63/93 (67%), Gaps = 2/93 (2%)
Query: 218 GNEPELYQVYKGRVSRVVDTGCFVQLNDFRGK-EGLVHVSQIATR-RIGNAKDVVKRDQE 275
G EP + +Y G+V+ ++ GCFVQL R + EGLVH+S++ R+ N DVV + Q
Sbjct: 7 GEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQR 66
Query: 276 VYVKVISVSGQKLSLSMRDVDQNTGKDLLPLKK 308
V VKV+S +G K SLSM+DVDQ TG+DL P ++
Sbjct: 67 VKVKVLSFTGTKTSLSMKDVDQETGEDLNPNRR 99
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 74.3 bits (181), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 41/86 (47%), Positives = 56/86 (65%), Gaps = 3/86 (3%)
Query: 219 NEPELYQVYKGRVSRVVDTGCFVQLNDFRGKEGLVHVSQIATRRIGNAKDVVKRDQEVYV 278
+E E+ ++Y G+V +VVD G FV N F K+GLVHVSQI+ R+ DV+K Q V V
Sbjct: 633 DEAEIGKIYDGKVVKVVDFGAFV--NFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKV 690
Query: 279 KVISVSGQ-KLSLSMRDVDQNTGKDL 303
K++ + K LSM+ VDQ TG+DL
Sbjct: 691 KLLGFDDRGKTKLSMKVVDQETGEDL 716
>pdb|4AM3|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
Length = 717
Score = 73.9 bits (180), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 41/86 (47%), Positives = 56/86 (65%), Gaps = 3/86 (3%)
Query: 219 NEPELYQVYKGRVSRVVDTGCFVQLNDFRGKEGLVHVSQIATRRIGNAKDVVKRDQEVYV 278
+E E+ ++Y G+V +VVD G FV N F K+GLVHVSQI+ R+ DV+K Q V V
Sbjct: 624 DEAEVGKIYDGKVVKVVDFGAFV--NFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKV 681
Query: 279 KVISVSGQ-KLSLSMRDVDQNTGKDL 303
K++ + K LSM+ VDQ TG+DL
Sbjct: 682 KLLGFDDRGKTKLSMKVVDQETGEDL 707
>pdb|4AID|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 73.6 bits (179), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 41/86 (47%), Positives = 56/86 (65%), Gaps = 3/86 (3%)
Query: 219 NEPELYQVYKGRVSRVVDTGCFVQLNDFRGKEGLVHVSQIATRRIGNAKDVVKRDQEVYV 278
+E E+ ++Y G+V +VVD G FV N F K+GLVHVSQI+ R+ DV+K Q V V
Sbjct: 633 DEAEVGKIYDGKVVKVVDFGAFV--NFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKV 690
Query: 279 KVISVSGQ-KLSLSMRDVDQNTGKDL 303
K++ + K LSM+ VDQ TG+DL
Sbjct: 691 KLLGFDDRGKTKLSMKVVDQETGEDL 716
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 64.3 bits (155), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 35/81 (43%), Positives = 54/81 (66%), Gaps = 3/81 (3%)
Query: 220 EPELYQVYKGRVSRVVDTGCFVQLNDFRGKEGLVHVSQIATRRIGNAKDVVKRDQEVYVK 279
E E+ +VY G+V+R+VD G FV + GKEGLVH+SQIA +R+ D ++ QEV VK
Sbjct: 624 EIEVGRVYTGKVTRIVDFGAFVAIGG--GKEGLVHISQIADKRVEKVTDYLQMGQEVPVK 681
Query: 280 VISVSGQ-KLSLSMRDVDQNT 299
V+ V Q ++ LS+++ + +
Sbjct: 682 VLEVDRQGRIRLSIKEATEQS 702
>pdb|2CQO|A Chain A, Solution Structure Of The S1 Rna Binding Domain Of Human
Hypothetical Protein Flj11067
Length = 119
Score = 63.5 bits (153), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 37/97 (38%), Positives = 59/97 (60%), Gaps = 5/97 (5%)
Query: 219 NEPELYQVYKGRVSRVVDTGCFVQLNDFRGKEGLVHVSQIATRRIGNAKDVVKRDQEVYV 278
N P LY +++G V+ V D G F+++ R K+GLVH + +++ R+ ++V +V+V
Sbjct: 18 NLPALYTIFQGEVAMVTDYGAFIKIPGCR-KQGLVHRTHMSSCRVDKPSEIVDVGDKVWV 76
Query: 279 KVISVSGQ----KLSLSMRDVDQNTGKDLLPLKKISE 311
K+I + K+SLSM+ V+Q TGKDL P I E
Sbjct: 77 KLIGREMKNDRIKVSLSMKVVNQGTGKDLDPNNVIIE 113
>pdb|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures
Length = 76
Score = 62.4 bits (150), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 35/76 (46%), Positives = 52/76 (68%), Gaps = 3/76 (3%)
Query: 220 EPELYQVYKGRVSRVVDTGCFVQLNDFRGKEGLVHVSQIATRRIGNAKDVVKRDQEVYVK 279
E E+ +VY G+V+R+VD G FV + GKEGLVH+SQIA +R+ D ++ QEV VK
Sbjct: 2 EIEVGRVYTGKVTRIVDFGAFVAIGG--GKEGLVHISQIADKRVEKVTDYLQMGQEVPVK 59
Query: 280 VISVSGQ-KLSLSMRD 294
V+ V Q ++ LS+++
Sbjct: 60 VLEVDRQGRIRLSIKE 75
>pdb|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From
Pyrococcus Horikoshii Ot3
Length = 275
Score = 55.1 bits (131), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/86 (34%), Positives = 50/86 (58%), Gaps = 2/86 (2%)
Query: 221 PELYQVYKGRVSRVVDTGCFVQLNDFRGKEGLVHVSQIATRRIGNAKDVVKRDQEVYVKV 280
PE + V R+ + G F++L+++ GKE +H+S++A+ + N +D +K Q+V KV
Sbjct: 9 PEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKV 68
Query: 281 ISVSGQK--LSLSMRDVDQNTGKDLL 304
I V +K + LS+R V Q K L
Sbjct: 69 IRVDPRKGHIDLSLRRVTQQQRKAKL 94
>pdb|1YZ6|A Chain A, Crystal Structure Of Intact Alpha Subunit Of Aif2 From
Pyrococcus Abyssi
Length = 274
Score = 55.1 bits (131), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 49/83 (59%), Gaps = 2/83 (2%)
Query: 221 PELYQVYKGRVSRVVDTGCFVQLNDFRGKEGLVHVSQIATRRIGNAKDVVKRDQEVYVKV 280
PE + V R+ + G F++L+++ GKE +H+S++A+ + N +D +K Q+V KV
Sbjct: 8 PEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKV 67
Query: 281 ISVSGQK--LSLSMRDVDQNTGK 301
I V +K + LS+R V Q K
Sbjct: 68 IRVDPRKGHIDLSLRRVTQQQRK 90
>pdb|2AHO|B Chain B, Structure Of The Archaeal Initiation Factor Eif2 Alpha-
Gamma Heterodimer From Sulfolobus Solfataricus Complexed
With Gdpnp
pdb|3CW2|C Chain C, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3CW2|D Chain D, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3CW2|G Chain G, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3CW2|H Chain H, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3V11|B Chain B, Structure Of The Ternary Initiation Complex
Aif2:gdpnp:methionylated Initiator Trna
Length = 266
Score = 44.3 bits (103), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 30/102 (29%), Positives = 56/102 (54%), Gaps = 3/102 (2%)
Query: 217 RGNEPELYQVYKGRVSRVVDTGCFVQLNDFRGKEGLVHVSQIATRRIGNAKDVVKRDQEV 276
R P ++ V +V D G +V L+++ G + + S+++++ + N +DV+K +++V
Sbjct: 5 RSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKV 64
Query: 277 YVKVISVSGQK--LSLSMRDV-DQNTGKDLLPLKKISEDDAL 315
VKVI V +K + +S++ V D K L KKI D +
Sbjct: 65 IVKVIRVDRRKGTVDVSLKKVTDDERRKKNLQWKKIQRLDKI 106
>pdb|1Q8K|A Chain A, Solution Structure Of Alpha Subunit Of Human Eif2
Length = 308
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 45/82 (54%), Gaps = 2/82 (2%)
Query: 216 YRGNEPELYQVYKGRVSRVVDTGCFVQLNDFRGKEGLVHVSQIATRRIGNAKDVVKRDQE 275
Y+ PE+ V V + + G +V L ++ EG++H+S+++ RRI + +++ +
Sbjct: 6 YQHKFPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRN 65
Query: 276 VYVKVISVSGQK--LSLSMRDV 295
VKVI V +K + LS R V
Sbjct: 66 ECVKVIRVDKEKGYIDLSKRRV 87
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 7/75 (9%)
Query: 221 PELYQVYKGRVSRVVDTGCFVQLNDFRGKEGLVHVSQI----ATRRIGNAKDVVKRDQEV 276
PE+ + G V + G FV L GK+GL+H+SQI +R+ N +DV+ Q+V
Sbjct: 665 PEVGERILGSVVKTTTFGAFVSL--LPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKV 722
Query: 277 YVKVISVSGQ-KLSL 290
V++ + + KLSL
Sbjct: 723 QVEIAEIDSRGKLSL 737
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 7/75 (9%)
Query: 221 PELYQVYKGRVSRVVDTGCFVQLNDFRGKEGLVHVSQI----ATRRIGNAKDVVKRDQEV 276
PE+ + G V + G FV L GK+GL+H+SQI +R+ N +DV+ Q+V
Sbjct: 665 PEVGERILGSVVKTTTFGAFVSL--LPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKV 722
Query: 277 YVKVISVSGQ-KLSL 290
V++ + + KLSL
Sbjct: 723 QVEIAEIDSRGKLSL 737
>pdb|2K4K|A Chain A, Solution Structure Of Gsp13 From Bacillus Subtilis
Length = 130
Score = 39.3 bits (90), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 44/74 (59%), Gaps = 4/74 (5%)
Query: 222 ELYQVYKGRVSRVVDTGCFVQLNDFRGKEGLVHVSQIATRRIGNAKDVVKRDQEVYVKVI 281
E+ VY G+V+ + G FV L++ +GLVH+S++ + + + + EV VKV+
Sbjct: 6 EVGSVYTGKVTGLQAYGAFVALDE--ETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVL 63
Query: 282 SVSGQ--KLSLSMR 293
+V + K+SLS+R
Sbjct: 64 AVDEEKGKISLSIR 77
>pdb|1GO3|E Chain E, Structure Of An Archeal Homolog Of The Eukaryotic Rna
Polymerase Ii Rpb4RPB7 COMPLEX
pdb|1GO3|M Chain M, Structure Of An Archeal Homolog Of The Eukaryotic Rna
Polymerase Ii Rpb4RPB7 COMPLEX
Length = 187
Score = 37.4 bits (85), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 26/38 (68%), Gaps = 3/38 (7%)
Query: 221 PELYQVYKGRVSRVVDTGCFVQLNDFRGKEGLVHVSQI 258
PE+Y++ +G V VV+ G FV+L +GL+HVSQI
Sbjct: 79 PEMYELIEGEVVDVVEFGSFVRLGPL---DGLIHVSQI 113
>pdb|3BZC|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas
Aeruginosa, Crystal Form I
pdb|3BZK|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas
Aeruginosa, Crystal Form 2
Length = 785
Score = 37.0 bits (84), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 4/73 (5%)
Query: 226 VYKGRVSRVVDTGCFVQLNDFRGKEGLVHVSQIATRRIGNAKDVVKRDQEVYVKVISVS- 284
V +G V+ V + G FV + ++GLVH+S ++ + + + +VVK V VKV+ V
Sbjct: 657 VLEGVVTNVTNFGAFVDIGVH--QDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDI 714
Query: 285 -GQKLSLSMRDVD 296
++ LSMR D
Sbjct: 715 PRNRVGLSMRMSD 727
>pdb|2OCE|A Chain A, Crystal Structure Of Tex Family Protein Pa5201 From
Pseudomonas Aeruginosa
Length = 780
Score = 37.0 bits (84), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 4/73 (5%)
Query: 226 VYKGRVSRVVDTGCFVQLNDFRGKEGLVHVSQIATRRIGNAKDVVKRDQEVYVKVISVS- 284
V +G V+ V + G FV + ++GLVH+S ++ + + + +VVK V VKV+ V
Sbjct: 658 VLEGVVTNVTNFGAFVDIGVH--QDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDI 715
Query: 285 -GQKLSLSMRDVD 296
++ LSMR D
Sbjct: 716 PRNRVGLSMRMSD 728
>pdb|2KHI|A Chain A, Nmr Structure Of The Domain 4 Of The E. Coli Ribosomal
Protein S1
Length = 115
Score = 36.2 bits (82), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 16/30 (53%), Positives = 23/30 (76%), Gaps = 2/30 (6%)
Query: 229 GRVSRVVDTGCFVQLNDFRGKEGLVHVSQI 258
GRV+ + D GCFV++ + G EGLVHVS++
Sbjct: 36 GRVTNLTDYGCFVEIEE--GVEGLVHVSEM 63
>pdb|1Q46|A Chain A, Crystal Structure Of The Eif2 Alpha Subunit From
Saccharomyces Cerevisia
Length = 175
Score = 36.2 bits (82), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 23/100 (23%), Positives = 51/100 (51%), Gaps = 12/100 (12%)
Query: 216 YRGNEPELYQVYKGRVSRVVDTGCFVQLNDFRGKEGLVHVSQIATRRIGNAKDVVKRDQE 275
Y PE+ + V ++ + G +V+L ++ EG++ +S+++ RRI + +
Sbjct: 8 YENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQ-------- 59
Query: 276 VYVKVISVSGQKLSLSMRDVDQNTGKDLLPLKKISEDDAL 315
K+I V +++ +R VD+ G L +++S +D +
Sbjct: 60 ---KLIRVGKNDVAVVLR-VDKEKGYIDLSKRRVSSEDII 95
>pdb|2A19|A Chain A, Pkr Kinase Domain- Eif2alpha- Amp-Pnp Complex.
pdb|2A1A|A Chain A, Pkr Kinase Domain-Eif2alpha Complex
Length = 175
Score = 35.8 bits (81), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 23/100 (23%), Positives = 51/100 (51%), Gaps = 12/100 (12%)
Query: 216 YRGNEPELYQVYKGRVSRVVDTGCFVQLNDFRGKEGLVHVSQIATRRIGNAKDVVKRDQE 275
Y PE+ + V ++ + G +V+L ++ EG++ +S+++ RRI + +
Sbjct: 8 YENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQ-------- 59
Query: 276 VYVKVISVSGQKLSLSMRDVDQNTGKDLLPLKKISEDDAL 315
K+I V +++ +R VD+ G L +++S +D +
Sbjct: 60 ---KLIRVGKNDVAVVLR-VDKEKGYIDLSKRRVSSEDII 95
>pdb|1UAA|A Chain A, E. Coli Rep HelicaseDNA COMPLEX
pdb|1UAA|B Chain B, E. Coli Rep HelicaseDNA COMPLEX
Length = 673
Score = 32.7 bits (73), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 38/129 (29%), Positives = 57/129 (44%), Gaps = 19/129 (14%)
Query: 543 VVIGETGSGKTTQVTQYLAEAGYTTRGKIGCT-QPRRVAAMSVAKRVAEEFGCRLGEEV- 600
+V+ GSGKT +T +A + RG C Q R +AA++ + A E R+G+ +
Sbjct: 19 LVLAGAGSGKTRVITNKIA---HLIRG---CGYQARHIAAVTFTNKAAREMKERVGQTLG 72
Query: 601 -----GYAIRFEDCTGPDTVIK-YMTDGMLLREILIDDNLSQYSVIMLDEAHERTIHTDV 654
G I G D + + Y GM L DD + +L E E I D
Sbjct: 73 RKEARGLMISTFHTLGLDIIKREYAALGMKANFSLFDDT---DQLALLKELTEGLIEDDK 129
Query: 655 LFGLLKQLV 663
+ LL+QL+
Sbjct: 130 V--LLQQLI 136
>pdb|2GZA|A Chain A, Crystal Structure Of The Virb11 Atpase From The Brucella
Suis Type Iv Secretion System In Complex With Sulphate
pdb|2GZA|B Chain B, Crystal Structure Of The Virb11 Atpase From The Brucella
Suis Type Iv Secretion System In Complex With Sulphate
pdb|2GZA|C Chain C, Crystal Structure Of The Virb11 Atpase From The Brucella
Suis Type Iv Secretion System In Complex With Sulphate
Length = 361
Score = 32.3 bits (72), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/37 (45%), Positives = 23/37 (62%)
Query: 532 LIQAVHDNQVLVVIGETGSGKTTQVTQYLAEAGYTTR 568
L +AV +V+VV GETGSGKTT + + E + R
Sbjct: 168 LRRAVQLERVIVVAGETGSGKTTLMKALMQEIPFDQR 204
>pdb|3ZVL|A Chain A, The Structural Basis For Substrate Recognition By
Mammalian Polynucleotide Kinase 3' Phosphatase
Length = 416
Score = 31.6 bits (70), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 3/52 (5%)
Query: 538 DNQVLVVIGETGSGKTTQVTQYLAEAGY--TTRGKIGCTQPRRVAAMSVAKR 587
+ +V+V +G G+GK+T + ++L AGY R +G Q R V++ A R
Sbjct: 257 NPEVVVAVGFPGAGKSTFIQEHLVSAGYVHVNRDTLGSWQ-RCVSSCQAALR 307
>pdb|3ZVN|A Chain A, The Structural Basis For Substrate Recognition By
Mammalian Polynucleotide Kinase 3' Phosphatase
Length = 416
Score = 31.6 bits (70), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 3/52 (5%)
Query: 538 DNQVLVVIGETGSGKTTQVTQYLAEAGY--TTRGKIGCTQPRRVAAMSVAKR 587
+ +V+V +G G+GK+T + ++L AGY R +G Q R V++ A R
Sbjct: 257 NPEVVVAVGFPGAGKSTFIQEHLVSAGYVHVNRDTLGSWQ-RCVSSCQAALR 307
>pdb|3ZVM|A Chain A, The Structural Basis For Substrate Recognition By
Mammalian Polynucleotide Kinase 3' Phosphatase
pdb|3ZVM|B Chain B, The Structural Basis For Substrate Recognition By
Mammalian Polynucleotide Kinase 3' Phosphatase
Length = 416
Score = 31.6 bits (70), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 3/52 (5%)
Query: 538 DNQVLVVIGETGSGKTTQVTQYLAEAGY--TTRGKIGCTQPRRVAAMSVAKR 587
+ +V+V +G G+GK+T + ++L AGY R +G Q R V++ A R
Sbjct: 257 NPEVVVAVGFPGAGKSTFIQEHLVSAGYVHVNRDTLGSWQ-RCVSSCQAALR 307
>pdb|1YJ5|A Chain A, Molecular Architecture Of Mammalian Polynucleotide Kinase,
A Dna Repair Enzyme
pdb|1YJ5|B Chain B, Molecular Architecture Of Mammalian Polynucleotide Kinase,
A Dna Repair Enzyme
Length = 383
Score = 31.6 bits (70), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 3/52 (5%)
Query: 538 DNQVLVVIGETGSGKTTQVTQYLAEAGY--TTRGKIGCTQPRRVAAMSVAKR 587
+ +V+V +G G+GK+T + ++L AGY R +G Q R V++ A R
Sbjct: 224 NPEVVVAVGFPGAGKSTFIQEHLVSAGYVHVNRDTLGSWQ-RCVSSCQAALR 274
>pdb|3U7E|B Chain B, Crystal Structure Of Mpnkp Catalytic Fragment (D170a)
pdb|3U7F|B Chain B, Crystal Structure Of Mpnkp Catalytic Fragment (D170a)
Bound To Single- Stranded Dna (Tcctcp)
pdb|3U7H|B Chain B, Crystal Structure Of Mpnkp Catalytic Fragment (D170a)
Bound To Single- Stranded Dna (Tccttp)
Length = 381
Score = 31.6 bits (70), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 3/52 (5%)
Query: 538 DNQVLVVIGETGSGKTTQVTQYLAEAGY--TTRGKIGCTQPRRVAAMSVAKR 587
+ +V+V +G G+GK+T + ++L AGY R +G Q R V++ A R
Sbjct: 222 NPEVVVAVGFPGAGKSTFIQEHLVSAGYVHVNRDTLGSWQ-RCVSSCQAALR 272
>pdb|3U7G|A Chain A, Crystal Structure Of Mpnkp Catalytic Fragment (D170a)
Bound To Single- Stranded Dna (Tcctap)
Length = 379
Score = 31.6 bits (70), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 3/52 (5%)
Query: 538 DNQVLVVIGETGSGKTTQVTQYLAEAGY--TTRGKIGCTQPRRVAAMSVAKR 587
+ +V+V +G G+GK+T + ++L AGY R +G Q R V++ A R
Sbjct: 220 NPEVVVAVGFPGAGKSTFIQEHLVSAGYVHVNRDTLGSWQ-RCVSSCQAALR 270
>pdb|4F4C|A Chain A, The Crystal Structure Of The Multi-Drug Transporter
Length = 1321
Score = 31.2 bits (69), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 34/149 (22%), Positives = 58/149 (38%), Gaps = 33/149 (22%)
Query: 487 VGLSAYDMPEWKKDAFGKALTFGQRSK------LSIQEQRQSL----------------P 524
+G + PE+ K F + FG K LS+ +++ L P
Sbjct: 1031 LGFATSYFPEYAKATFAGGIIFGMLRKISKIDSLSLAGEKKKLYGKVIFKNVRFAYPERP 1090
Query: 525 IYKLKKELIQAVHDNQVLVVIGETGSGKTTQVTQYLAEAGYTTRG--------KIGCTQP 576
++ K L +V Q L ++G +G GK+T V L E Y T G +I P
Sbjct: 1091 EIEILKGLSFSVEPGQTLALVGPSGCGKSTVVA--LLERFYDTLGGEIFIDGSEIKTLNP 1148
Query: 577 RRV-AAMSVAKRVAEEFGCRLGEEVGYAI 604
+ +++ + F C + E + Y +
Sbjct: 1149 EHTRSQIAIVSQEPTLFDCSIAENIIYGL 1177
>pdb|2QEQ|A Chain A, Crystal Structure Of Kunjin Virus Ns3 Helicase
pdb|2QEQ|B Chain B, Crystal Structure Of Kunjin Virus Ns3 Helicase
Length = 434
Score = 30.4 bits (67), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 22/112 (19%), Positives = 45/112 (40%), Gaps = 16/112 (14%)
Query: 540 QVLVVIGETGSGKTTQVTQYLAEAGYTTRGKIGCTQPRRVAAMSVAKRVAEEFGCRLGEE 599
Q+ V+ G+GKT ++ + + R + P RV A +A+ +
Sbjct: 3 QITVLDLHPGAGKTRRILPQIIKEAINRRLRTAVLAPTRVVAAEMAEALR---------- 52
Query: 600 VGYAIRFEDCT-----GPDTVIKYMTDGMLLREILIDDNLSQYSVIMLDEAH 646
G IR++ + ++ M L ++ + Y++ ++DEAH
Sbjct: 53 -GLPIRYQTSAVAREHNGNEIVDVMCHATLTHRLMSPHRVPNYNLFVMDEAH 103
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 30.0 bits (66), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 529 KKELIQAVHDNQVLVVIGETGSGKTTQVTQYLAEAGYTTRG-KIGCTQPRRVAAMSVAKR 587
K+ ++ A+ ++ ++ G G+GKTT V + + +A +G K+ C P +A ++ +R
Sbjct: 195 KEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQA--VKQGLKVLCCAPSNIAVDNLVER 252
Query: 588 VA 589
+A
Sbjct: 253 LA 254
>pdb|4B3G|A Chain A, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
pdb|4B3G|B Chain B, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
Length = 646
Score = 30.0 bits (66), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 529 KKELIQAVHDNQVLVVIGETGSGKTTQVTQYLAEAGYTTRG-KIGCTQPRRVAAMSVAKR 587
K+ ++ A+ ++ ++ G G+GKTT V + + +A +G K+ C P +A ++ +R
Sbjct: 195 KEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQA--VKQGLKVLCCAPSNIAVDNLVER 252
Query: 588 VA 589
+A
Sbjct: 253 LA 254
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
0.318 0.136 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 31,278,589
Number of Sequences: 62578
Number of extensions: 1263759
Number of successful extensions: 3442
Number of sequences better than 100.0: 38
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 3383
Number of HSP's gapped (non-prelim): 52
length of query: 1176
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1066
effective length of database: 8,089,757
effective search space: 8623680962
effective search space used: 8623680962
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.6 bits)