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= 021437
(312 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3G6S|A Chain A, Crystal Structure Of The
EndonucleaseEXONUCLEASEPHOSPHATASE (BVU_0621) FROM
Bacteroides Vulgatus. Northeast Structural Genomics
Consortium Target Bvr56d
Length = 267
Score = 102 bits (255), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 73/238 (30%), Positives = 102/238 (42%), Gaps = 24/238 (10%)
Query: 9 TFNLHEDQQEDSPNSWVKRRDLCISVITSYSPMILCTQQGVKSQLDYLQQCLPAYDQFGV 68
TFN+ D +DS N+W R+D I + I+ Q+ + +Q L+ LP YD GV
Sbjct: 8 TFNIRYDNPQDSLNNWQYRKDRVCQFIKDHELDIVGXQEVLHNQFQDLRAGLPEYDGIGV 67
Query: 69 SRKGPEDTSDEHCTIFYDKEKVELLEGGTFWLSESPSVPGSKAWGAEVPCIATWATFQLK 128
R + T+ E+ +FY K+K E+L+ TFWL+E+P G W A IATWA F+ K
Sbjct: 68 GRDDGK-TAGEYAPLFYRKDKYEVLDSNTFWLAENPDSVGXXGWDAVCVRIATWAKFKDK 126
Query: 129 GVEPPGFSFQIVNTNMDEFTXXXXXXXXLLTWQHIASLPPSLPVIYCGGFNTQKES---- 184
G F VNT+ D LL + I + P + G FN S
Sbjct: 127 AT---GKIFXAVNTHFDHVGEEARRQSALLIIRKIKEIVGERPAVVTGDFNVTDASDAYE 183
Query: 185 --TTGRFLLGRSREHGVVGDMRDAWPNARMRKNVSLIRTYHGFKGNKQGALEFLKLIF 240
TT F+ +DA+ A V T+H F E + IF
Sbjct: 184 TITTNEFV------------XKDAYKTAARVTGVDY--TFHDFARIPAEDCEKIDFIF 227
>pdb|3MPR|A Chain A, Crystal Structure Of EndonucleaseEXONUCLEASEPHOSPHATASE
FAMILY Protein From Bacteroides Thetaiotaomicron,
Northeast Structural Genomics Consortium Target Btr318a
pdb|3MPR|B Chain B, Crystal Structure Of EndonucleaseEXONUCLEASEPHOSPHATASE
FAMILY Protein From Bacteroides Thetaiotaomicron,
Northeast Structural Genomics Consortium Target Btr318a
pdb|3MPR|C Chain C, Crystal Structure Of EndonucleaseEXONUCLEASEPHOSPHATASE
FAMILY Protein From Bacteroides Thetaiotaomicron,
Northeast Structural Genomics Consortium Target Btr318a
pdb|3MPR|D Chain D, Crystal Structure Of EndonucleaseEXONUCLEASEPHOSPHATASE
FAMILY Protein From Bacteroides Thetaiotaomicron,
Northeast Structural Genomics Consortium Target Btr318a
Length = 298
Score = 92.8 bits (229), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 58/184 (31%), Positives = 84/184 (45%), Gaps = 9/184 (4%)
Query: 3 VALSLMTFNLHEDQQEDSP--NSWVKRRDLCISVITSYSPMILCTQQGVKSQLDYLQQCL 60
+L++ ++NL DS + W +R + + + I TQ+ QL ++ L
Sbjct: 5 TSLTVASYNLRNANGSDSARGDGWGQRYPVIAQXVQYHDFDIFGTQECFLHQLKDXKEAL 64
Query: 61 PAYDQFGVSRKGPEDTSDEHCTIFYDKEKVELLEGGTFWLSESPSVPGSKAWGAEVPCIA 120
P YD GV R +D EH IFY +K +++E G FWLSE+P VP SK W A +P I
Sbjct: 65 PGYDYIGVGRDDGKDKG-EHSAIFYRTDKFDIVEKGDFWLSETPDVP-SKGWDAVLPRIC 122
Query: 121 TWATFQLKGVEPPGFSFQIVNTNMDEFTXXXXXXXXLLTWQHIASL--PPSLPVIYCGGF 178
+W F+ K GF F N + D L + L +LP I G F
Sbjct: 123 SWGHFKCKDT---GFEFLFFNLHXDHIGKKARVESAFLVQEKXKELGRGKNLPAILTGDF 179
Query: 179 NTQK 182
N +
Sbjct: 180 NVDQ 183
>pdb|3L1W|A Chain A, The Crystal Structure Of A Functionally Unknown Conserved
Protein From Enterococcus Faecalis V583
pdb|3L1W|B Chain B, The Crystal Structure Of A Functionally Unknown Conserved
Protein From Enterococcus Faecalis V583
pdb|3L1W|C Chain C, The Crystal Structure Of A Functionally Unknown Conserved
Protein From Enterococcus Faecalis V583
pdb|3L1W|D Chain D, The Crystal Structure Of A Functionally Unknown Conserved
Protein From Enterococcus Faecalis V583
pdb|3L1W|E Chain E, The Crystal Structure Of A Functionally Unknown Conserved
Protein From Enterococcus Faecalis V583
pdb|3L1W|F Chain F, The Crystal Structure Of A Functionally Unknown Conserved
Protein From Enterococcus Faecalis V583
Length = 257
Score = 68.2 bits (165), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 68/289 (23%), Positives = 120/289 (41%), Gaps = 44/289 (15%)
Query: 6 SLMTFNLHEDQQEDSPNSWVKRRDLCISVITSYSPMILCTQQGVKSQLDYLQQCLPAYDQ 65
+ T+N+ D + D W R++ +I + + C Q+ +Q+ + L AY
Sbjct: 2 KIATYNVRVDTEYDQDWQWSFRKEAVCQLINFHDWSLCCIQEVRPNQV----RDLKAYTT 57
Query: 66 FG-VSRKGPEDTSDEHCTIFYDKEKVELLEGGTFWLSESPSVPGSKAWGAEVPCIATWAT 124
F +S + D E I Y+++KV+ ++ G FWLSE+P P A P IA W
Sbjct: 58 FTCLSAEREGDGQGEGLAILYNEQKVQAIDTGYFWLSETPQQPSIHP-EAGCPRIALWGL 116
Query: 125 FQLKGVEPPGFSFQIVNTNMDEFTXXXXXXXXLLTWQHIASLPPSLPVIYCGGFNTQKES 184
F+ P F ++N ++D + + + + P + G FN +
Sbjct: 117 FKETTQNTP---FLVINVHLDHISAHARLAGXTVILEELHDKIAQYPTLLXGDFNAES-- 171
Query: 185 TTGRFLLGRSREHGVVGDMRDAWPNARMRKNVSLIRTYHGFKGNKQGALEFLKLIFRALC 244
G V +D+ KN++ T++G +G Q
Sbjct: 172 -------GEEVHQLVQKKFQDS-------KNLA---THYGPRGTFQN------------- 201
Query: 245 LCWDRQTQDL-HIDWILFRGRSLIPGSCEVVNDNIDGYYPSSHYPIFAE 292
+ + +L ID+I +G + + + D+IDG +PS H+P+ AE
Sbjct: 202 FTYTKPWAELEEIDYIYVKGWQVQQTAS--LTDSIDGRFPSDHFPLEAE 248
>pdb|3ZGB|A Chain A, Greater Efficiency Of Photosynthetic Carbon Fixation Due
To Single Amino Acid Substitution
pdb|3ZGB|B Chain B, Greater Efficiency Of Photosynthetic Carbon Fixation Due
To Single Amino Acid Substitution
Length = 972
Score = 32.0 bits (71), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 29/63 (46%), Gaps = 11/63 (17%)
Query: 199 VVGDMRDAWPNARMRKNVSLIRTYHGFKG--------NKQGALEFLKLIFRALCLCWDRQ 250
++GD+RD N R R L HG N + LE L+L +R+LC C DR
Sbjct: 374 ILGDVRDKLYNTRERSRHLLA---HGISDIPEEAVYTNVEQFLEPLELCYRSLCDCGDRV 430
Query: 251 TQD 253
D
Sbjct: 431 IAD 433
>pdb|2CKF|B Chain B, Crystal Structure Of The Terminal Component Of The Pah-
Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1
pdb|2CKF|D Chain D, Crystal Structure Of The Terminal Component Of The Pah-
Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1
pdb|2CKF|F Chain F, Crystal Structure Of The Terminal Component Of The Pah-
Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1
Length = 174
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 11/66 (16%)
Query: 60 LPAYDQFGVSRKGPEDTSDEHCTIFYD-----KEKVELLEGGTFWLSESPS-----VPGS 109
+P Y+Q V + P+ T D+ I+ D K++VE L G W+ + PS V
Sbjct: 48 MPIYEQRFVRDRRPDPTPDD-AAIYNDDFEELKQRVERLYSGQVWMEDPPSKIRYFVSNV 106
Query: 110 KAWGAE 115
+A+ AE
Sbjct: 107 EAFEAE 112
>pdb|3ZGE|A Chain A, Greater Efficiency Of Photosynthetic Carbon Fixation Due
To Single Amino Acid Substitution
pdb|3ZGE|B Chain B, Greater Efficiency Of Photosynthetic Carbon Fixation Due
To Single Amino Acid Substitution
Length = 990
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 5/60 (8%)
Query: 199 VVGDMRDAWPNARMRKNVSLIRTY-----HGFKGNKQGALEFLKLIFRALCLCWDRQTQD 253
++GD+RD N R R L+ N + LE L+L +R+LC C D D
Sbjct: 392 ILGDVRDKLYNTRERSRHLLVDGKSDIPDEAVYTNVEQLLEPLELCYRSLCDCGDHVIAD 451
>pdb|2GBW|B Chain B, Crystal Structure Of Biphenyl 2,3-Dioxygenase From
Sphingomonas Yanoikuyae B1
pdb|2GBW|D Chain D, Crystal Structure Of Biphenyl 2,3-Dioxygenase From
Sphingomonas Yanoikuyae B1
pdb|2GBW|F Chain F, Crystal Structure Of Biphenyl 2,3-Dioxygenase From
Sphingomonas Yanoikuyae B1
pdb|2GBX|B Chain B, Crystal Structure Of Biphenyl 2,3-Dioxygenase From
Sphingomonas Yanoikuyae B1 Bound To Biphenyl
pdb|2GBX|D Chain D, Crystal Structure Of Biphenyl 2,3-Dioxygenase From
Sphingomonas Yanoikuyae B1 Bound To Biphenyl
pdb|2GBX|F Chain F, Crystal Structure Of Biphenyl 2,3-Dioxygenase From
Sphingomonas Yanoikuyae B1 Bound To Biphenyl
Length = 174
Score = 28.1 bits (61), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 6/51 (11%)
Query: 60 LPAYDQFGVSRKGPEDTSDEHCTIFYD-----KEKVELLEGGTFWLSESPS 105
+P Y+Q + P+ T D+ I+ D K++VE L G W+ + PS
Sbjct: 48 MPIYEQRLTRDRRPDPTPDD-AAIYNDDFGELKQRVERLYSGQVWMEDPPS 97
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 0.436
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,841,464
Number of Sequences: 62578
Number of extensions: 415771
Number of successful extensions: 770
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 761
Number of HSP's gapped (non-prelim): 9
length of query: 312
length of database: 14,973,337
effective HSP length: 99
effective length of query: 213
effective length of database: 8,778,115
effective search space: 1869738495
effective search space used: 1869738495
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: 51 (24.3 bits)