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= 006051
(663 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 = 271 bits (694), Expect = 7e-73, Method: Compositional matrix adjust.
Identities = 190/576 (32%), Positives = 313/576 (54%), Gaps = 40/576 (6%)
Query: 40 LYIDFAELLDEDPEIAHLVFSKPADYLRFFEDAAIWAHKIVFDELKSCEKRVEKKFIHVR 99
L I+F+++L + +A+ + + L E A++ H + D + ++ +EK +HVR
Sbjct: 39 LIIEFSDVLSFNENLAYEIINNTKIILPILE-GALYDHILQLD--PTYQRDIEK--VHVR 93
Query: 100 INVSGSPLECPETFPSIGRVRVKHHGVLLTLKGTVIRSGATK--MYEGERTYMCRKCKHM 157
I + P + ++R G L+T+ G +++ K +Y+ ++ C
Sbjct: 94 I------VGIPRVI-ELRKIRSTDIGKLITIDGILVKVTPVKERIYKATYKHIHPDCMQE 146
Query: 158 FPVYPELETRNSIV-LPSHCPSQRSKPCEGTNFQFVENSIICHDYQEIKIQESTQVLGVG 216
F +PE E ++ +P+ CP + KP + F+ + D+Q+ IQE + + G
Sbjct: 147 FE-WPEDEEMPEVLEMPTICP-KCGKPGQ---FRLIPEKTKLIDWQKAVIQERPEEVPSG 201
Query: 217 VIPRSILVILKDDLVDIVKAGDDVIVTGILTAKW-SPDLKDVRCDLDPVLIANHVRRTNE 275
+PR + +IL+DDLVD + GD V VTGIL K SP + R D + + + + +
Sbjct: 202 QLPRQLEIILEDDLVDSARPGDRVKVTGILDIKQDSPVKRGSRAVFDIYMKVSSIEVSQK 261
Query: 276 LKSDIDIPDDIIMQFKQFWSEFKDTPLKGRNAILRGICPQVFGLFTVKLAVALTLIGGVQ 335
+ ++ I ++ + K KD ++ R I+ I P ++G + +K A+AL L GGV
Sbjct: 262 VLDEVIISEEDEKKIKDLA---KDPWIRDR--IISSIAPSIYGHWELKEALALALFGGVP 316
Query: 336 HVDASGTKVRGESHLLLVGDPGTGKSQFLKFAAKLSNRSVIXXXXXXXXXXXXXXAVKDG 395
V T++RG+ H+L++GDPGT KSQ L+F ++++ R+V V++
Sbjct: 317 KV-LEDTRIRGDIHILIIGDPGTAKSQMLQFISRVAPRAVYTTGKGSTAAGLTAAVVREK 375
Query: 396 G--EWMLEAGALVLADGGLCCIDEFDSMREHDRATIHEAMEQQTISVAKAGLVTTLSTRT 453
G E+ LEAGALVLADGG+ IDE D MR+ DR IHEAMEQQT+S+AKAG+V L+ R
Sbjct: 376 GTGEYYLEAGALVLADGGIAVIDEIDKMRDEDRVAIHEAMEQQTVSIAKAGIVAKLNARA 435
Query: 454 IIFGATNPK-GHYDPNLSLSVNTTLSGPLLSRFDIVLVLLDTKNPEWDAVVSSHILAEGG 512
+ A NPK G Y +S N L +LSRFD++ +L D E D ++++IL
Sbjct: 436 AVIAAGNPKFGRYISERPVSDNINLPPTILSRFDLIFILKDQPG-EQDRELANYIL---D 491
Query: 513 LSEEKDTEPLTDIWPLAMLRRYIYFVKGYFKPILTKEAEKVISSYYQLQRRSATQNAAR- 571
+ K T+ + DI LR+YI + + Y P +T EA+ +I+ ++ R+ +++
Sbjct: 492 VHSGKSTKNIIDI---DTLRKYIAYARKYVTPKITSEAKNLITDFFVEMRKKSSETPDSP 548
Query: 572 --TTVRMLESLIRLAQAHARLMFRNEVTRLDAITAI 605
T R LE+LIR+++A+A++ + EVTR DA AI
Sbjct: 549 ILITPRQLEALIRISEAYAKMALKAEVTREDAERAI 584
>pdb|3F8T|A Chain A, Crystal Structure Analysis Of A Full-Length Mcm Homolog
From Methanopyrus Kandleri
Length = 506
Score = 82.8 bits (203), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 78/276 (28%), Positives = 118/276 (42%), Gaps = 35/276 (12%)
Query: 349 HLLLVGDPGTGKSQFLKFAAKLSNRSVIXXXXXXXXXXXXXXAVKDGGEWMLEAGALVLA 408
H+LL G P L+ R V +D G W L AGA VLA
Sbjct: 241 HVLLAGYPVVCSEILHHVLDHLAPRGVYVDLRRTELTDLTAVLKEDRG-WALRAGAAVLA 299
Query: 409 DGGLCCIDEFDSMREHDRATIHEAMEQQTISVAKAGLVTTLSTRTIIFGATNPKGHY--D 466
DGG+ +D + E R + EAM++ T++V L+ R + A NP + D
Sbjct: 300 DGGILAVDHLEGAPEPHRWALMEAMDKGTVTVDG----IALNARCAVLAAINPGEQWPSD 355
Query: 467 PNLSLSVNTTLSGPLLSRFDIVLVLLDTKNPEWDAVVSSHILAEGGLSEEKDTEPLTDIW 526
P ++ L LS FD++ L P G EE+DTE +
Sbjct: 356 PPIA---RIDLDQDFLSHFDLIAFLGVDPRP--------------GEPEEQDTE----VP 394
Query: 527 PLAMLRRY-IYFVKGYFKPILTKEAEKVISSYYQLQRRSATQNAAR------TTVRMLES 579
+LRRY +Y ++ + P LT+EA K + +Y+ +R + T R LES
Sbjct: 395 SYTLLRRYLLYAIREHPAPELTEEARKRLEHWYETRREEVEERLGMGLPTLPVTRRQLES 454
Query: 580 LIRLAQAHARLMFRNEVTRLDAITAILCIESSMTTS 615
+ RLA+AHAR+ ++V D A ++ + T+
Sbjct: 455 VERLAKAHARMRLSDDVEPEDVDIAAELVDWYLETA 490
>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 = 70.1 bits (170), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 63/214 (29%), Positives = 98/214 (45%), Gaps = 30/214 (14%)
Query: 37 HYP----LYIDFAELLDEDPEIAHLVFSKPADYLRFFEDAAIWAHKIVFDELKSCEKRVE 92
YP + +D+ +L DP++A L+ KP D +R AA A + + D L+
Sbjct: 37 KYPNVRSIEVDYLDLEMFDPDLADLLIEKPDDVIR----AAQQAIRNI-DRLR------- 84
Query: 93 KKFIHVRINVSGSPLECPETFPSIGRVRVKHHGVLLTLKGTVIRSGATKMYEGERTYMCR 152
K + + I SG P + +R K G + + G V ++ + + + CR
Sbjct: 85 -KNVDLNIRFSGISNVIP-----LRELRSKFIGKFVAVDGIVRKTDEIRPRIVKAVFECR 138
Query: 153 KCKHMFPVYPELETRNSIVLPSHCPSQRSKPCEGTNFQFVENSIICHDYQEIKIQESTQV 212
C V ++ N I PS C C G +F+ +++ D Q +K+QE +
Sbjct: 139 GCMRHHAV---TQSTNMITEPSLCSE-----CGGRSFRLLQDESEFLDTQTLKLQEPLEN 190
Query: 213 LGVGVIPRSILVILKDDLVDIVKAGDDVIVTGIL 246
L G PR I V+L+DDLVD + GD V VTG L
Sbjct: 191 LSGGEQPRQITVVLEDDLVDTLTPGDIVRVTGTL 224
>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 = 65.9 bits (159), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 61/219 (27%), Positives = 109/219 (49%), Gaps = 20/219 (9%)
Query: 40 LYIDFAELLDEDPEIAHLVFSKPADYLRFFEDAAIWAHKIVFDELKSCEKRVEKKFIHVR 99
L I+F+++L + +A+ + + L E A++ H + D + ++ +EK +HVR
Sbjct: 45 LIIEFSDVLSFNENLAYEIINNTKIILPILE-GALYDHILQLD--PTYQRDIEK--VHVR 99
Query: 100 INVSGSPLECPETFPSIGRVRVKHHGVLLTLKGTVIRSGATK--MYEGERTYMCRKCKHM 157
I G P + ++R G L+T+ G +++ K +Y+ ++ C
Sbjct: 100 I--VGIP-----RVIELRKIRSTDIGKLITIDGILVKVTPVKERIYKATYKHIHPDCMQE 152
Query: 158 FPVYPELETRNSIV-LPSHCPSQRSKPCEGTNFQFVENSIICHDYQEIKIQESTQVLGVG 216
F +PE E ++ +P+ CP + KP + F+ + D+Q+ IQE + + G
Sbjct: 153 FE-WPEDEEMPEVLEMPTICP-KCGKPGQ---FRLIPEKTKLIDWQKAVIQERPEEVPSG 207
Query: 217 VIPRSILVILKDDLVDIVKAGDDVIVTGILTAKWSPDLK 255
+PR + +IL+DDLVD + GD V VTGIL K +K
Sbjct: 208 QLPRQLEIILEDDLVDSARPGDRVKVTGILDIKQDSPVK 246
>pdb|3K1J|A Chain A, Crystal Structure Of Lon Protease From Thermococcus
Onnurineus Na1
pdb|3K1J|B Chain B, Crystal Structure Of Lon Protease From Thermococcus
Onnurineus Na1
Length = 604
Score = 32.3 bits (72), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 24/41 (58%)
Query: 330 LIGGVQHVDASGTKVRGESHLLLVGDPGTGKSQFLKFAAKL 370
+IG V+ T + H+LL+G+PGTGKS + A+L
Sbjct: 43 VIGQEHAVEVIKTAANQKRHVLLIGEPGTGKSMLGQAMAEL 83
>pdb|3ZQ4|A Chain A, Unusual, Dual Endo- And Exo-Nuclease Activity In The
Degradosome Explained By Crystal Structure Analysis Of
Rnase J1
pdb|3ZQ4|C Chain C, Unusual, Dual Endo- And Exo-Nuclease Activity In The
Degradosome Explained By Crystal Structure Analysis Of
Rnase J1
pdb|3ZQ4|D Chain D, Unusual, Dual Endo- And Exo-Nuclease Activity In The
Degradosome Explained By Crystal Structure Analysis Of
Rnase J1
pdb|3ZQ4|E Chain E, Unusual, Dual Endo- And Exo-Nuclease Activity In The
Degradosome Explained By Crystal Structure Analysis Of
Rnase J1
Length = 555
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 25/91 (27%), Positives = 40/91 (43%), Gaps = 12/91 (13%)
Query: 555 SSYYQLQR--RSATQNAARTTV--RMLESLIRLAQAHARL-------MFRNEVTRLDA-I 602
S+ ++LQ+ +A QN + V R +ES I + Q + + NE+ R+ A
Sbjct: 233 SNIHRLQQVIEAAVQNGRKVAVFGRSMESAIEIGQTLGYINCPKNTFIEHNEINRMPANK 292
Query: 603 TAILCIESSMTTSAIVDSVGNALHSNFTENP 633
ILC S A + + N H + NP
Sbjct: 293 VTILCTGSQGEPMAALSRIANGTHRQISINP 323
>pdb|1VQW|A Chain A, Crystal Structure Of A Protein With Similarity To Flavin-
Containing Monooxygenases And To Mammalian
Dimethylalanine Monooxygenases
pdb|1VQW|B Chain B, Crystal Structure Of A Protein With Similarity To Flavin-
Containing Monooxygenases And To Mammalian
Dimethylalanine Monooxygenases
Length = 457
Score = 30.0 bits (66), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 34/110 (30%), Positives = 44/110 (40%), Gaps = 19/110 (17%)
Query: 159 PVYPELETRNSIVLPSHCPSQRSKPCEGTNFQFVENSIICHDYQEIKIQESTQVLGVGVI 218
P+Y +L+T I L +C Q KP QF I +YQ I Q
Sbjct: 85 PLYRDLQTNTPIELXGYC-DQSFKP---QTLQFPHRHTI-QEYQRIYAQ----------- 128
Query: 219 PRSILVILKDDLVDIVKAGDDVIVTGILTAKWSPDLKDVRCDLDPVLIAN 268
P + L D++DI K +VT T SP KD+ D V I N
Sbjct: 129 PLLPFIKLATDVLDIEKKDGSWVVTYKGTKAGSPISKDI---FDAVSICN 175
>pdb|2GV8|A Chain A, Crystal Structure Of Flavin-Containing Monooxygenase (Fmo)
From S.Pombe And Nadph Cofactor Complex
pdb|2GV8|B Chain B, Crystal Structure Of Flavin-Containing Monooxygenase (Fmo)
From S.Pombe And Nadph Cofactor Complex
pdb|2GVC|A Chain A, Crystal Structure Of Flavin-Containing Monooxygenase
(Fmo)from S.Pombe And Substrate (Methimazole) Complex
pdb|2GVC|B Chain B, Crystal Structure Of Flavin-Containing Monooxygenase
(Fmo)from S.Pombe And Substrate (Methimazole) Complex
pdb|2GVC|D Chain D, Crystal Structure Of Flavin-Containing Monooxygenase
(Fmo)from S.Pombe And Substrate (Methimazole) Complex
pdb|2GVC|E Chain E, Crystal Structure Of Flavin-Containing Monooxygenase
(Fmo)from S.Pombe And Substrate (Methimazole) Complex
Length = 447
Score = 29.6 bits (65), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 34/110 (30%), Positives = 44/110 (40%), Gaps = 19/110 (17%)
Query: 159 PVYPELETRNSIVLPSHCPSQRSKPCEGTNFQFVENSIICHDYQEIKIQESTQVLGVGVI 218
P+Y +L+T I L +C Q KP QF I +YQ I Q
Sbjct: 83 PLYRDLQTNTPIELXGYC-DQSFKP---QTLQFPHRHTI-QEYQRIYAQ----------- 126
Query: 219 PRSILVILKDDLVDIVKAGDDVIVTGILTAKWSPDLKDVRCDLDPVLIAN 268
P + L D++DI K +VT T SP KD+ D V I N
Sbjct: 127 PLLPFIKLATDVLDIEKKDGSWVVTYKGTKAGSPISKDI---FDAVSICN 173
>pdb|1HQC|A Chain A, Structure Of Ruvb From Thermus Thermophilus Hb8
pdb|1HQC|B Chain B, Structure Of Ruvb From Thermus Thermophilus Hb8
Length = 324
Score = 29.6 bits (65), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 39/162 (24%), Positives = 60/162 (37%), Gaps = 35/162 (21%)
Query: 336 HVDASGTKVRGESHLLLVGDPGTGKSQFLKFAAKLSNRSVIXXXXXXXXXXXXXXAVKDG 395
+++A+ + HLLL G PG GK+ VI A++
Sbjct: 27 YLEAAKARKEPLEHLLLFGPPGLGKTTLA---------HVIAHELGVNLRVTSGPAIEKP 77
Query: 396 GEWMLEAGALVLA----DGGLCCIDEFDSMREHDRATIHEAMEQ--QTISVAKAGLVTTL 449
G+ A +LA +G + IDE + ++ AME I + + T+
Sbjct: 78 GDL-----AAILANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTI 132
Query: 450 S---TRTIIFGATNPKGHYDPNLSLSVNTTLSGPLLSRFDIV 488
R + GAT G ++ PLLSRF IV
Sbjct: 133 RLELPRFTLIGATTRPG------------LITAPLLSRFGIV 162
>pdb|3O3M|B Chain B, (R)-2-Hydroxyisocaproyl-Coa Dehydratase
pdb|3O3M|D Chain D, (R)-2-Hydroxyisocaproyl-Coa Dehydratase
pdb|3O3N|B Chain B, (R)-2-Hydroxyisocaproyl-Coa Dehydratase In Complex With
Its Substrate (R)-2-Hydroxyisocaproyl-Coa
pdb|3O3N|D Chain D, (R)-2-Hydroxyisocaproyl-Coa Dehydratase In Complex With
Its Substrate (R)-2-Hydroxyisocaproyl-Coa
pdb|3O3O|B Chain B, (R)-2-Hydroxyisocaproyl-Coa Dehydratase In Complex With
(R)-2- Hydroxyisocaproate
Length = 385
Score = 29.6 bits (65), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 38/70 (54%), Gaps = 3/70 (4%)
Query: 234 VKAGDDVIVTGILTAKWSPDLKDVRCDLDPVLIANHV-RRTNELKSDIDIPDDIIMQFKQ 292
V +G V++TGIL S D+ D+ D + ++A+ + + T + ++D+ DD + + +
Sbjct: 226 VCSGKKVLLTGILAD--SKDILDILEDNNISVVADDLAQETRQFRTDVPAGDDALERLAR 283
Query: 293 FWSEFKDTPL 302
WS + L
Sbjct: 284 QWSNIEGCSL 293
>pdb|1IXS|B Chain B, Structure Of Ruvb Complexed With Ruva Domain Iii
Length = 318
Score = 29.3 bits (64), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 39/162 (24%), Positives = 60/162 (37%), Gaps = 35/162 (21%)
Query: 336 HVDASGTKVRGESHLLLVGDPGTGKSQFLKFAAKLSNRSVIXXXXXXXXXXXXXXAVKDG 395
+++A+ + HLLL G PG GK+ VI A++
Sbjct: 27 YLEAAKARKEPLEHLLLFGPPGLGKTTLA---------HVIAHELGVNLRVTSGPAIEKP 77
Query: 396 GEWMLEAGALVLA----DGGLCCIDEFDSMREHDRATIHEAMEQ--QTISVAKAGLVTTL 449
G+ A +LA +G + IDE + ++ AME I + + T+
Sbjct: 78 GDL-----AAILANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTI 132
Query: 450 S---TRTIIFGATNPKGHYDPNLSLSVNTTLSGPLLSRFDIV 488
R + GAT G ++ PLLSRF IV
Sbjct: 133 RLELPRFTLIGATTRPG------------LITAPLLSRFGIV 162
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
0.321 0.137 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,087,215
Number of Sequences: 62578
Number of extensions: 765558
Number of successful extensions: 1941
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1923
Number of HSP's gapped (non-prelim): 20
length of query: 663
length of database: 14,973,337
effective HSP length: 105
effective length of query: 558
effective length of database: 8,402,647
effective search space: 4688677026
effective search space used: 4688677026
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)