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= 011953
(474 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 = 206 bits (525), Expect = 2e-53, Method: Compositional matrix adjust.
Identities = 144/433 (33%), Positives = 234/433 (54%), Gaps = 30/433 (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 VLDEVIISEEDEKKIKDL---AKDPWIRDR--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-GHY 465
+ A NPK G Y
Sbjct: 436 AVIAAGNPKFGRY 448
>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 = 69.7 bits (169), Expect = 3e-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 = 65.5 bits (158), 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|3F8T|A Chain A, Crystal Structure Analysis Of A Full-Length Mcm Homolog
From Methanopyrus Kandleri
Length = 506
Score = 48.9 bits (115), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 36/124 (29%), Positives = 51/124 (41%), Gaps = 7/124 (5%)
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 PNLC 470
P +
Sbjct: 356 PPIA 359
>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 = 0.52, 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|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 = 30.0 bits (66), Expect = 3.2, 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|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 = 29.6 bits (65), Expect = 3.8, 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 = 4.1, 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
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
0.322 0.139 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,309,911
Number of Sequences: 62578
Number of extensions: 576888
Number of successful extensions: 1449
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1440
Number of HSP's gapped (non-prelim): 10
length of query: 474
length of database: 14,973,337
effective HSP length: 102
effective length of query: 372
effective length of database: 8,590,381
effective search space: 3195621732
effective search space used: 3195621732
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)