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= 002353
(932 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3F9V|A Chain A, Crystal Structure Of A Near Full-Length Archaeal Mcm:
Functional Insights For An Aaa+ Hexameric Helicase
Length = 595
Score = 400 bits (1028), Expect = e-111, Method: Compositional matrix adjust.
Identities = 237/613 (38%), Positives = 356/613 (58%), Gaps = 41/613 (6%)
Query: 215 FKEFLLTYVSPKSEQGDFEYVRLINEIVSANKCSLEIDYKQFIYIHPNIAIWLADAPQSV 274
F EFL T+ K +Y+ INE+V+ K SL I++ + + N+A + + + +
Sbjct: 8 FIEFLTTF---KGNNNQNKYIERINELVAYRKKSLIIEFSDVLSFNENLAYEIINNTKII 64
Query: 275 LEVMEDVARNVVFNLHPNYKRIHQKIYVRITNLPVYDQIRNIRQIHLNTMIRIGGVVTRR 334
L ++E + + L P Y+R +K++VRI +P ++R IR + +I I G++ +
Sbjct: 65 LPILEGALYDHILQLDPTYQRDIEKVHVRIVGIPRVIELRKIRSTDIGKLITIDGILVKV 124
Query: 335 TGVFPQLQQVKY-----DCNKCGAILGPFFQNSYSEVKVGS-CPECQSKGPFTINIEQTI 388
T V ++ + Y DC + P + +++ + CP+C G F + E+T
Sbjct: 125 TPVKERIYKATYKHIHPDCMQ--EFEWPEDEEMPEVLEMPTICPKCGKPGQFRLIPEKTK 182
Query: 389 YRNYQKLTLQESPGIVPAGRLPRYKEVILLNDLIDCARPGEEIEVTGIYTNNFDLSLNTK 448
++QK +QE P VP+G+LPR E+IL +DL+D ARPG+ ++VTGI D S +
Sbjct: 183 LIDWQKAVIQERPEEVPSGQLPRQLEIILEDDLVDSARPGDRVKVTGILDIKQD-SPVKR 241
Query: 449 NGFPVFATVVEANHITKKHDLFSAYKLTQEDKEEIEKLAKDPRIGERIIKSIAPSIYGHE 508
VF ++ + I + +++ED+++I+ LAKDP I +RII SIAPSIYGH
Sbjct: 242 GSRAVFDIYMKVSSIEVSQKVLDEVIISEEDEKKIKDLAKDPWIRDRIISSIAPSIYGHW 301
Query: 509 DIKTALALSMFGGQEKNVKGKHRLRGDINVLLLGDPGTAKSQFLKYVEKTGQRAVYTTGK 568
++K ALAL++FGG K V R+RGDI++L++GDPGTAKSQ L+++ + RAVYTTGK
Sbjct: 302 ELKEALALALFGGVPK-VLEDTRIRGDIHILIIGDPGTAKSQMLQFISRVAPRAVYTTGK 360
Query: 569 GASAVGLTAAVHKDPVTREWTLEGGALVLADRGICLIDEFDKMNDQDRVSIHEAMEQQSI 628
G++A GLTAAV ++ T E+ LE GALVLAD GI +IDE DKM D+DRV+IHEAMEQQ++
Sbjct: 361 GSTAAGLTAAVVREKGTGEYYLEAGALVLADGGIAVIDEIDKMRDEDRVAIHEAMEQQTV 420
Query: 629 SISKAGIVTSLQARCSVIAAANPVGGRYDSSKTFSENVELTDPIISRFXXXXXXXXXXXX 688
SI+KAGIV L AR +VIAA NP GRY S + S+N+ L I+SRF
Sbjct: 421 SIAKAGIVAKLNARAAVIAAGNPKFGRYISERPVSDNINLPPTILSRFDLIFILKDQPGE 480
Query: 689 XXXEMLAKFVIDSHFKSQPKGVNLDDKSKNESEEDIQVADREIDPEILPQDLLKKYITYA 748
E LA +++D H K I+ D L+KYI YA
Sbjct: 481 QDRE-LANYILDVHSGKSTKN-------------------------IIDIDTLRKYIAYA 514
Query: 749 KLNVFPRLHDPDMEKLTHVYAELRRESSHGQGVPIAV--RHIESMIRMSEAHARMRLRQH 806
+ V P++ +T + E+R++SS PI + R +E++IR+SEA+A+M L+
Sbjct: 515 RKYVTPKITSEAKNLITDFFVEMRKKSSETPDSPILITPRQLEALIRISEAYAKMALKAE 574
Query: 807 VTQEDVNMAIRVL 819
VT+ED AI ++
Sbjct: 575 VTREDAERAINIM 587
>pdb|2VL6|A Chain A, Structural Analysis Of The Sulfolobus Solfataricus Mcm
Protein N-Terminal Domain
pdb|2VL6|B Chain B, Structural Analysis Of The Sulfolobus Solfataricus Mcm
Protein N-Terminal Domain
pdb|2VL6|C Chain C, Structural Analysis Of The Sulfolobus Solfataricus Mcm
Protein N-Terminal Domain
Length = 268
Score = 116 bits (290), Expect = 6e-26, Method: Compositional matrix adjust.
Identities = 72/228 (31%), Positives = 125/228 (54%), Gaps = 11/228 (4%)
Query: 215 FKEFLLTYVSPKSEQGDFEYVRLINEIVSANKCSLEIDYKQFIYIHPNIAIWLADAPQSV 274
F EFL T+ K +Y+ INE+V+ K SL I++ + + N+A + + + +
Sbjct: 14 FIEFLTTF---KGNNNQNKYIERINELVAYRKKSLIIEFSDVLSFNENLAYEIINNTKII 70
Query: 275 LEVMEDVARNVVFNLHPNYKRIHQKIYVRITNLPVYDQIRNIRQIHLNTMIRIGGVVTRR 334
L ++E + + L P Y+R +K++VRI +P ++R IR + +I I G++ +
Sbjct: 71 LPILEGALYDHILQLDPTYQRDIEKVHVRIVGIPRVIELRKIRSTDIGKLITIDGILVKV 130
Query: 335 TGVFPQLQQVKY-----DCNKCGAILGPFFQNSYSEVKVGS-CPECQSKGPFTINIEQTI 388
T V ++ + Y DC + P + +++ + CP+C G F + E+T
Sbjct: 131 TPVKERIYKATYKHIHPDCMQ--EFEWPEDEEMPEVLEMPTICPKCGKPGQFRLIPEKTK 188
Query: 389 YRNYQKLTLQESPGIVPAGRLPRYKEVILLNDLIDCARPGEEIEVTGI 436
++QK +QE P VP+G+LPR E+IL +DL+D ARPG+ ++VTGI
Sbjct: 189 LIDWQKAVIQERPEEVPSGQLPRQLEIILEDDLVDSARPGDRVKVTGI 236
>pdb|3F8T|A Chain A, Crystal Structure Analysis Of A Full-Length Mcm Homolog
From Methanopyrus Kandleri
Length = 506
Score = 105 bits (262), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 113/406 (27%), Positives = 177/406 (43%), Gaps = 79/406 (19%)
Query: 427 PGEEIEVTGIYTNNFDLSLNTKNGFPVFATVVEANHITKKHDLFSAYKLTQEDKEEIEKL 486
PG +E+ GI V + ++A + KK + + E +E E
Sbjct: 157 PGLRVEILGI----------------VRSATLDALEVHKKDPIPEVHPDPAELEEFRELA 200
Query: 487 AKDPRIGERIIKSIAPSIYGHEDIKTALALSMFGGQEKNVKGKHRLRGDINVLLLGDPGT 546
KDP ++IAP + G E++ LAL +F KN + H VLL G P
Sbjct: 201 DKDPLT--TFARAIAP-LPGAEEVGKMLALQLFSCVGKNSERLH-------VLLAGYPVV 250
Query: 547 AKSQFLKYVEKTGQRAVYTTGKGASAVGLTAAVHKDPVTREWTLEGGALVLADRGICLID 606
++ R VY + LTA + +D R W L GA VLAD GI +D
Sbjct: 251 CSEILHHVLDHLAPRGVYVDLRRTELTDLTAVLKED---RGWALRAGAAVLADGGILAVD 307
Query: 607 EFDKMNDQDRVSIHEAMEQQSISISKAGIVTSLQARCSVIAAANPVGGRYDSSKTFSENV 666
+ + R ++ EAM++ ++++ GI +L ARC+V+AA NP G ++ S
Sbjct: 308 HLEGAPEPHRWALMEAMDKGTVTVD--GI--ALNARCAVLAAINP-GEQWPS-------- 354
Query: 667 ELTDPIISRFXXXXXXXXXXXXXXXEMLAKFVIDSHFKSQPKGVNLDDKSKNESEEDIQV 726
DP I+R + L+ F + + P+ E EE
Sbjct: 355 ---DPPIARI-----------DLDQDFLSHFDLIAFLGVDPR--------PGEPEEQ--- 389
Query: 727 ADREIDPEILPQDLLKKYITYA-KLNVFPRLHDPDMEKLTHVYAELRRESSHGQG----- 780
D E+ LL++Y+ YA + + P L + ++L H Y R E G
Sbjct: 390 -----DTEVPSYTLLRRYLLYAIREHPAPELTEEARKRLEHWYETRREEVEERLGMGLPT 444
Query: 781 VPIAVRHIESMIRMSEAHARMRLRQHVTQEDVNMAIRVLLDSFIST 826
+P+ R +ES+ R+++AHARMRL V EDV++A L+D ++ T
Sbjct: 445 LPVTRRQLESVERLAKAHARMRLSDDVEPEDVDIAAE-LVDWYLET 489
>pdb|1LTL|A Chain A, The Dodecamer Structure Of Mcm From Archaeal M.
Thermoautotrophicum
pdb|1LTL|B Chain B, The Dodecamer Structure Of Mcm From Archaeal M.
Thermoautotrophicum
pdb|1LTL|C Chain C, The Dodecamer Structure Of Mcm From Archaeal M.
Thermoautotrophicum
pdb|1LTL|D Chain D, The Dodecamer Structure Of Mcm From Archaeal M.
Thermoautotrophicum
pdb|1LTL|E Chain E, The Dodecamer Structure Of Mcm From Archaeal M.
Thermoautotrophicum
pdb|1LTL|F Chain F, The Dodecamer Structure Of Mcm From Archaeal M.
Thermoautotrophicum
Length = 279
Score = 79.7 bits (195), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 61/251 (24%), Positives = 116/251 (46%), Gaps = 14/251 (5%)
Query: 248 SLEIDYKQFIYIHPNIAIWLADAPQSVLEVMEDVARNVVFNLHPNYKRIHQKIYVRITNL 307
S+E+DY P++A L + P V+ + RN+ + R + + +R + +
Sbjct: 43 SIEVDYLDLEMFDPDLADLLIEKPDDVIRAAQQAIRNI------DRLRKNVDLNIRFSGI 96
Query: 308 PVYDQIRNIRQIHLNTMIRIGGVVTRRTGVFPQLQQVKYDCNKCGAILGPFFQNSYSEVK 367
+R +R + + + G+V + + P++ + ++C C Q++ +
Sbjct: 97 SNVIPLRELRSKFIGKFVAVDGIVRKTDEIRPRIVKAVFECRGCMR-HHAVTQSTNMITE 155
Query: 368 VGSCPECQSKGPFTINIEQTIYRNYQKLTLQESPGIVPAGRLPRYKEVILLNDLIDCARP 427
C EC + F + +++ + + Q L LQE + G PR V+L +DL+D P
Sbjct: 156 PSLCSECGGRS-FRLLQDESEFLDTQTLKLQEPLENLSGGEQPRQITVVLEDDLVDTLTP 214
Query: 428 GEEIEVTGIYTNNFDLSLNTKNGFPVFATVVEANHITKKHDLFSAYKLTQEDKEEIEKLA 487
G+ + VTG D TK F + N+ F ++++ED+E+I++LA
Sbjct: 215 GDIVRVTGTLRTVRD--ERTKR----FKNFIYGNYTEFLEQEFEELQISEEDEEKIKELA 268
Query: 488 KDPRIGERIIK 498
DP I E+II+
Sbjct: 269 GDPNIYEKIIR 279
>pdb|3DZD|A Chain A, Crystal Structure Of Sigma54 Activator Ntrc4 In The
Inactive State
pdb|3DZD|B Chain B, Crystal Structure Of Sigma54 Activator Ntrc4 In The
Inactive State
Length = 368
Score = 32.3 bits (72), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 46/199 (23%), Positives = 78/199 (39%), Gaps = 38/199 (19%)
Query: 458 VEANHITKKHDLFSAYKLTQEDKEEIEKLAKDPRIGERIIKSIAPSIYGHEDIKTALALS 517
VE +T KH F Y +EEIE + + P+I E IK + P I
Sbjct: 105 VERFLLTIKHA-FEEYSKKAPPQEEIEFVGEHPKILE--IKRLIPKI------------- 148
Query: 518 MFGGQEKNVKGKHRLRGDINVLLLGDPGTAKSQFLKYVEK-TGQRAVYTTGKGAS----- 571
+ VL+ G+ GT K + + + +G++ + AS
Sbjct: 149 --------------AKSKAPVLITGESGTGKEIVARLIHRYSGRKGAFVDLNCASIPQEL 194
Query: 572 AVGLTAAVHKDPVTREWTLEGGALVLADRGICLIDEFDKMNDQDRVSIHEAMEQQSISIS 631
A K T T + G L LAD+G +DE +++ + + + +E + S +
Sbjct: 195 AESELFGHEKGAFTGALTRKKGKLELADQGTLFLDEVGELDQRVQAKLLRVLE--TGSFT 252
Query: 632 KAGIVTSLQARCSVIAAAN 650
+ G ++ VI+A N
Sbjct: 253 RLGGNQKIEVDIRVISATN 271
>pdb|2CSD|A Chain A, Crystal Structure Of Topoisomerase V (61 Kda Fragment)
pdb|2CSD|B Chain B, Crystal Structure Of Topoisomerase V (61 Kda Fragment)
Length = 519
Score = 30.0 bits (66), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 7/61 (11%)
Query: 482 EIEKLAKDPRIGERIIKSIAP------SIYGHEDIKTALALSMFGGQEK-NVKGKHRLRG 534
EIEKLA +GER+++S+ P SI G + + L +GG K G LR
Sbjct: 445 EIEKLASVEGVGERVLRSLVPGYASLISIRGIDRERAERLLKKYGGYSKVREAGVEELRE 504
Query: 535 D 535
D
Sbjct: 505 D 505
>pdb|2CSB|A Chain A, Crystal Structure Of Topoisomerase V From Methanopyrus
Kandleri (61 Kda Fragment)
pdb|2CSB|B Chain B, Crystal Structure Of Topoisomerase V From Methanopyrus
Kandleri (61 Kda Fragment)
Length = 519
Score = 30.0 bits (66), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 7/61 (11%)
Query: 482 EIEKLAKDPRIGERIIKSIAP------SIYGHEDIKTALALSMFGGQEK-NVKGKHRLRG 534
EIEKLA +GER+++S+ P SI G + + L +GG K G LR
Sbjct: 445 EIEKLASVEGVGERVLRSLVPGYASLISIRGIDRERAERLLKKYGGYSKVREAGVEELRE 504
Query: 535 D 535
D
Sbjct: 505 D 505
>pdb|3D3F|A Chain A, Crystal Structure Of Yvgn And Cofactor Nadph From Bacillus
Subtilis
pdb|3D3F|B Chain B, Crystal Structure Of Yvgn And Cofactor Nadph From Bacillus
Subtilis
Length = 275
Score = 29.6 bits (65), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 443 LSLNTKNGFPVFATVVEANHITKKHDLFSAYKLTQEDKEEIEKLAKDPRIG 493
L + ++G ++ + I + D+F ++L+QED ++I+ L KD R+G
Sbjct: 218 LRWDLQHGVVTIPKSIKEHRIIENADIFD-FELSQEDMDKIDALNKDERVG 267
>pdb|4GFJ|A Chain A, Crystal Structure Of Topo-78, An N-Terminal 78kda Fragment
Of Topoisomerase V
Length = 685
Score = 29.6 bits (65), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 7/61 (11%)
Query: 482 EIEKLAKDPRIGERIIKSIAP------SIYGHEDIKTALALSMFGGQEK-NVKGKHRLRG 534
EIEKLA +GER+++S+ P SI G + + L +GG K G LR
Sbjct: 445 EIEKLASVEGVGERVLRSLVPGYASLISIRGIDRERAERLLKKYGGYSKVREAGVEELRE 504
Query: 535 D 535
D
Sbjct: 505 D 505
>pdb|3F7J|A Chain A, B.Subtilis Yvgn
pdb|3F7J|B Chain B, B.Subtilis Yvgn
Length = 276
Score = 29.6 bits (65), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 443 LSLNTKNGFPVFATVVEANHITKKHDLFSAYKLTQEDKEEIEKLAKDPRIG 493
L + ++G ++ + I + D+F ++L+QED ++I+ L KD R+G
Sbjct: 219 LRWDLQHGVVTIPKSIKEHRIIENADIFD-FELSQEDMDKIDALNKDERVG 268
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 0.135 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,359,773
Number of Sequences: 62578
Number of extensions: 953195
Number of successful extensions: 2489
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 2471
Number of HSP's gapped (non-prelim): 19
length of query: 932
length of database: 14,973,337
effective HSP length: 108
effective length of query: 824
effective length of database: 8,214,913
effective search space: 6769088312
effective search space used: 6769088312
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)