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= 005024
(718 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 = 313 bits (803), Expect = 2e-85, Method: Compositional matrix adjust.
Identities = 212/635 (33%), Positives = 326/635 (51%), Gaps = 69/635 (10%)
Query: 15 EFISNFADANGDAKYANILQDVANRKIRSIQIDLEDLFNYKDFDEEFFRRVTENTRRYIG 74
EF++ F N KY + ++ + +S+ I+ D+ + F+E + NT+ +
Sbjct: 10 EFLTTFKGNNNQNKYIERINELVAYRKKSLIIEFSDVLS---FNENLAYEIINNTKIILP 66
Query: 75 IFASAI-DELLPEPTEAFPDDDHDILMTQRSEDGADNTDGADPRQKMPPEIKRYYE-VYI 132
I A+ D +L ++ P +R E V++
Sbjct: 67 ILEGALYDHIL----------------------------------QLDPTYQRDIEKVHV 92
Query: 133 RASSKGRPFSIREVKASYIGQLVRISGIITRCSDVKPLMQVAVY------TCEECGFEIY 186
R R +R+++++ IG+L+ I GI+ + + VK + A Y +E +
Sbjct: 93 RIVGIPRVIELRKIRSTDIGKLITIDGILVKVTPVKERIYKATYKHIHPDCMQEFEWPED 152
Query: 187 QEVTARVFMPLFECPSQRCKINKTKGNLVLQLRASKFLKFQEAKIQELAEHVPKGHIPRT 246
+E+ + MP CP +C G L +K + +Q+A IQE E VP G +PR
Sbjct: 153 EEMPEVLEMPTI-CP--KCG---KPGQFRLIPEKTKLIDWQKAVIQERPEEVPSGQLPRQ 206
Query: 247 MTVHLRGELTRKVAPGDVVEFSGIF-----LPIPYTGFRALRAGLVADTYLEAMSVTHFK 301
+ + L +L PGD V+ +GI P+ R RA V D Y++ S+ +
Sbjct: 207 LEIILEDDLVDSARPGDRVKVTGILDIKQDSPVK----RGSRA--VFDIYMKVSSIEVSQ 260
Query: 302 KKYXXXXXXXXXXXHISRLAEDGDIYNKLARSLAPEIYGHEDIKKALLLLLVGAPHRKLK 361
K I LA+D I +++ S+AP IYGH ++K+AL L L G + L+
Sbjct: 261 KVLDEVIISEEDEKKIKDLAKDPWIRDRIISSIAPSIYGHWELKEALALALFGGVPKVLE 320
Query: 362 DGMKIRGDLHICLMGDPGVAKSQLLKHIINVAPRGVYTTGRGSSGVGLTAAVQRDNVTNE 421
D +IRGD+HI ++GDPG AKSQ+L+ I VAPR VYTTG+GS+ GLTAAV R+ T E
Sbjct: 321 D-TRIRGDIHILIIGDPGTAKSQMLQFISRVAPRAVYTTGKGSTAAGLTAAVVREKGTGE 379
Query: 422 MVLEGGALVLADMGICAIDEFDKMDESDRTAIHEVMEQQTVSIAKAGITTSLNARTAVLS 481
LE GALVLAD GI IDE DKM + DR AIHE MEQQTVSIAKAGI LNAR AV++
Sbjct: 380 YYLEAGALVLADGGIAVIDEIDKMRDEDRVAIHEAMEQQTVSIAKAGIVAKLNARAAVIA 439
Query: 482 AANPAWGRYDLRRTPAENINLPPALLSRFDLLWLILDRADMDSDLEMARHVVYVHQNKES 541
A NP +GRY R ++NINLPP +LSRFDL++++ D+ + D E+A +++ VH K +
Sbjct: 440 AGNPKFGRYISERPVSDNINLPPTILSRFDLIFILKDQPG-EQDRELANYILDVHSGKST 498
Query: 542 PALGFTPLEPAILRAYISAARR-LSPCVPRELEEYIAAAYSNIRQEEAKSNTPHSYTTVR 600
+ ++ LR YI+ AR+ ++P + E + I + +R++ +++ T R
Sbjct: 499 KNI----IDIDTLRKYIAYARKYVTPKITSEAKNLITDFFVEMRKKSSETPDSPILITPR 554
Query: 601 TXXXXXXXXXXXXXXXFSETVAQSDVDEALRLMQM 635
V + D + A+ +M++
Sbjct: 555 QLEALIRISEAYAKMALKAEVTREDAERAINIMRL 589
>pdb|3F8T|A Chain A, Crystal Structure Analysis Of A Full-Length Mcm Homolog
From Methanopyrus Kandleri
Length = 506
Score = 87.4 bits (215), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 82/237 (34%), Positives = 113/237 (47%), Gaps = 21/237 (8%)
Query: 278 GFRALRAGLVADTYLEAMSVTHFKKKYXXXXXXXXXXXHISRLAEDGDIYNKLARSLAPE 337
G R G+V L+A+ V H K LA D D AR++AP
Sbjct: 158 GLRVEILGIVRSATLDALEV-HKKDPIPEVHPDPAELEEFRELA-DKDPLTTFARAIAP- 214
Query: 338 IYGHEDIKKALLLLLVGAPHRKLKDGMKIRGDLHICLMGDPGVAKSQLLKHIIN-VAPRG 396
+ G E++ K L L L + + LH+ L G P V S++L H+++ +APRG
Sbjct: 215 LPGAEEVGKMLALQLFSCVGKNSER-------LHVLLAGYP-VVCSEILHHVLDHLAPRG 266
Query: 397 VYTTGRGSSGVGLTAAVQRDNVTNEMVLEGGALVLADMGICAIDEFDKMDESDRTAIHEV 456
VY R + LTA ++ D L GA VLAD GI A+D + E R A+ E
Sbjct: 267 VYVDLRRTELTDLTAVLKEDR---GWALRAGAAVLADGGILAVDHLEGAPEPHRWALMEA 323
Query: 457 MEQQTVSIAKAGITTSLNARTAVLSAANPAWGRYDLRRTPAENINLPPALLSRFDLL 513
M++ TV++ GI +LNAR AVL+A NP G P I+L LS FDL+
Sbjct: 324 MDKGTVTV--DGI--ALNARCAVLAAINP--GEQWPSDPPIARIDLDQDFLSHFDLI 374
>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 = 69.7 bits (169), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 63/265 (23%), Positives = 113/265 (42%), Gaps = 51/265 (19%)
Query: 15 EFISNFADANGDAKYANILQDVANRKIRSIQIDLEDLFNYKDFDEEFFRRVTENTRRYIG 74
EF++ F N KY + ++ + +S+ I+ D+ + F+E + NT+ +
Sbjct: 16 EFLTTFKGNNNQNKYIERINELVAYRKKSLIIEFSDVLS---FNENLAYEIINNTKIILP 72
Query: 75 IFASAI-DELLPEPTEAFPDDDHDILMTQRSEDGADNTDGADPRQKMPPEIKRYYE-VYI 132
I A+ D +L ++ P +R E V++
Sbjct: 73 ILEGALYDHIL----------------------------------QLDPTYQRDIEKVHV 98
Query: 133 RASSKGRPFSIREVKASYIGQLVRISGIITRCSDVKPLMQVAVY------TCEECGFEIY 186
R R +R+++++ IG+L+ I GI+ + + VK + A Y +E +
Sbjct: 99 RIVGIPRVIELRKIRSTDIGKLITIDGILVKVTPVKERIYKATYKHIHPDCMQEFEWPED 158
Query: 187 QEVTARVFMPLFECPSQRCKINKTKGNLVLQLRASKFLKFQEAKIQELAEHVPKGHIPRT 246
+E+ + MP CP +C G L +K + +Q+A IQE E VP G +PR
Sbjct: 159 EEMPEVLEMPTI-CP--KCG---KPGQFRLIPEKTKLIDWQKAVIQERPEEVPSGQLPRQ 212
Query: 247 MTVHLRGELTRKVAPGDVVEFSGIF 271
+ + L +L PGD V+ +GI
Sbjct: 213 LEIILEDDLVDSARPGDRVKVTGIL 237
>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 = 67.0 bits (162), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 60/222 (27%), Positives = 103/222 (46%), Gaps = 17/222 (7%)
Query: 48 LEDLFNYKDFDEEFFRRVTENTRRYIGIFASAIDELLPEPTEAFPDDDHDILMTQRSEDG 107
E+ F+ +D+ + RV E +Y + + +D L E F D D+L+ E
Sbjct: 18 FEEFFSLQDYKD----RVFEAIEKYPNVRSIEVDYL---DLEMFDPDLADLLI----EKP 66
Query: 108 ADNTDGADPRQKMPPEIKRYYEVYIRASSKGRPFSIREVKASYIGQLVRISGIITRCSDV 167
D A + +++ ++ IR S +RE+++ +IG+ V + GI+ + ++
Sbjct: 67 DDVIRAAQQAIRNIDRLRKNVDLNIRFSGISNVIPLRELRSKFIGKFVAVDGIVRKTDEI 126
Query: 168 KPLMQVAVYTCEECGFEIYQEVTARVFMPLFECPSQRCKINKTKGNLVLQLRASKFLKFQ 227
+P + AV+ C C + VT M PS C + +LQ S+FL Q
Sbjct: 127 RPRIVKAVFECRGCMR--HHAVTQSTNM--ITEPSL-CSECGGRSFRLLQ-DESEFLDTQ 180
Query: 228 EAKIQELAEHVPKGHIPRTMTVHLRGELTRKVAPGDVVEFSG 269
K+QE E++ G PR +TV L +L + PGD+V +G
Sbjct: 181 TLKLQEPLENLSGGEQPRQITVVLEDDLVDTLTPGDIVRVTG 222
>pdb|1IN5|A Chain A, Thermogota Maritima Ruvb A156s Mutant
Length = 334
Score = 32.7 bits (73), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 16/71 (22%)
Query: 326 IYNKLARSLAP----EIYGHEDIKKALLLLLVGAPHRKLKDGMKIRGDL--HICLMGDPG 379
+Y+ + L P E G E++KK L L L A K+RG++ H+ L G PG
Sbjct: 11 VYDSGVQFLRPKSLDEFIGQENVKKKLSLALEAA---------KMRGEVLDHVLLAGPPG 61
Query: 380 VAKSQLLKHII 390
+ K+ L HII
Sbjct: 62 LGKTT-LAHII 71
>pdb|1IN4|A Chain A, Thermotoga Maritima Ruvb Holliday Junction Branch
Migration Motor
Length = 334
Score = 32.7 bits (73), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 16/71 (22%)
Query: 326 IYNKLARSLAP----EIYGHEDIKKALLLLLVGAPHRKLKDGMKIRGDL--HICLMGDPG 379
+Y+ + L P E G E++KK L L L A K+RG++ H+ L G PG
Sbjct: 11 VYDSGVQFLRPKSLDEFIGQENVKKKLSLALEAA---------KMRGEVLDHVLLAGPPG 61
Query: 380 VAKSQLLKHII 390
+ K+ L HII
Sbjct: 62 LGKTT-LAHII 71
>pdb|1IN7|A Chain A, Thermotoga Maritima Ruvb R170a
Length = 334
Score = 32.7 bits (73), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 16/71 (22%)
Query: 326 IYNKLARSLAP----EIYGHEDIKKALLLLLVGAPHRKLKDGMKIRGDL--HICLMGDPG 379
+Y+ + L P E G E++KK L L L A K+RG++ H+ L G PG
Sbjct: 11 VYDSGVQFLRPKSLDEFIGQENVKKKLSLALEAA---------KMRGEVLDHVLLAGPPG 61
Query: 380 VAKSQLLKHII 390
+ K+ L HII
Sbjct: 62 LGKTT-LAHII 71
>pdb|1J7K|A Chain A, Thermotoga Maritima Ruvb P216g Mutant
Length = 334
Score = 32.7 bits (73), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 16/71 (22%)
Query: 326 IYNKLARSLAP----EIYGHEDIKKALLLLLVGAPHRKLKDGMKIRGDL--HICLMGDPG 379
+Y+ + L P E G E++KK L L L A K+RG++ H+ L G PG
Sbjct: 11 VYDSGVQFLRPKSLDEFIGQENVKKKLSLALEAA---------KMRGEVLDHVLLAGPPG 61
Query: 380 VAKSQLLKHII 390
+ K+ L HII
Sbjct: 62 LGKTT-LAHII 71
>pdb|1IN8|A Chain A, Thermotoga Maritima Ruvb T158v
Length = 334
Score = 32.3 bits (72), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 16/71 (22%)
Query: 326 IYNKLARSLAP----EIYGHEDIKKALLLLLVGAPHRKLKDGMKIRGDL--HICLMGDPG 379
+Y+ + L P E G E++KK L L L A K+RG++ H+ L G PG
Sbjct: 11 VYDSGVQFLRPKSLDEFIGQENVKKKLSLALEAA---------KMRGEVLDHVLLAGPPG 61
Query: 380 VAKSQLLKHII 390
+ K+ L HII
Sbjct: 62 LGKTT-LAHII 71
>pdb|3JYL|A Chain A, Crystal Structures Of Pseudomonas Syringae Pv. Tomato
Dc3000 Quinone Oxidoreductase
pdb|3JYN|A Chain A, Crystal Structures Of Pseudomonas Syringae Pv. Tomato
Dc3000 Quinone Oxidoreductase Complexed With Nadph
Length = 325
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 39/84 (46%), Gaps = 20/84 (23%)
Query: 339 YGHEDIKKALLLLLVGAPHRKLKDGMKIRGDLHICLMGDPGVAKSQLLKHIINVAPRG-V 397
Y HED+ K +L +L DG K C + GV + L + +VAPRG V
Sbjct: 192 YSHEDVAKRVL---------ELTDGKK-------CPVVYDGVGQDTWLTSLDSVAPRGLV 235
Query: 398 YTTGRGS---SGVGLTAAVQRDNV 418
+ G S SGV L Q+D+V
Sbjct: 236 VSFGNASGPVSGVNLGILAQKDSV 259
>pdb|1IN6|A Chain A, Thermotoga Maritima Ruvb K64r Mutant
Length = 334
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 16/71 (22%)
Query: 326 IYNKLARSLAP----EIYGHEDIKKALLLLLVGAPHRKLKDGMKIRGDL--HICLMGDPG 379
+Y+ + L P E G E++KK L L L A K+RG++ H+ L G PG
Sbjct: 11 VYDSGVQFLRPKSLDEFIGQENVKKKLSLALEAA---------KMRGEVLDHVLLAGPPG 61
Query: 380 VAKSQLLKHII 390
+ ++ L HII
Sbjct: 62 LGRTT-LAHII 71
>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 = 30.8 bits (68), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 414 QRDNVTNEMVLEGGALVLADMGICAIDEFDKMDESDRTAIHEVMEQQTVSIAKAGITTSL 473
++ T + + G L LAD G +DE ++D+ + + V+E T S + G +
Sbjct: 203 EKGAFTGALTRKKGKLELADQGTLFLDEVGELDQRVQAKLLRVLE--TGSFTRLGGNQKI 260
Query: 474 NARTAVLSAAN 484
V+SA N
Sbjct: 261 EVDIRVISATN 271
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
0.320 0.135 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,952,835
Number of Sequences: 62578
Number of extensions: 818897
Number of successful extensions: 1879
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1865
Number of HSP's gapped (non-prelim): 15
length of query: 718
length of database: 14,973,337
effective HSP length: 106
effective length of query: 612
effective length of database: 8,340,069
effective search space: 5104122228
effective search space used: 5104122228
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: 55 (25.8 bits)