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= psy5867
(287 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1JHJ|A Chain A, Crystal Structure Of The Apc10DOC1 SUBUNIT OF THE HUMAN
Anaphase-Promoting Complex
Length = 171
Score = 219 bits (559), Expect = 1e-57, Method: Compositional matrix adjust.
Identities = 103/176 (58%), Positives = 125/176 (71%), Gaps = 23/176 (13%)
Query: 10 DPVMEERLGRIREVGSQAIWSLSSCKPGFGVDQLRDDCMDTYWQSDGQLPHLVNVQFRRK 69
DP ER G +RE+GSQA+WSLSSCKPGFGVDQLRDD ++TYWQSDG PHLVN
Sbjct: 11 DPKQLERTGTVREIGSQAVWSLSSCKPGFGVDQLRDDNLETYWQSDGSQPHLVN------ 64
Query: 70 TTVQDICIYRQLPHLVNVQFRRKTTVQDICIYTDYKLDESYTPSRVSVRAGTNFNDLQEI 129
+QFRRKTTV+ +CIY DYK DESYTPS++SVR G NF++LQEI
Sbjct: 65 -----------------IQFRRKTTVKTLCIYADYKSDESYTPSKISVRVGNNFHNLQEI 107
Query: 130 EVVDLNEPSGWVXXXXXXXXXXXXRTYMIQIAVMSNHQNGRDTHMRQIKVYSPVQQ 185
++L EPSGW+ RT+MIQIAV++NHQNGRDTHMRQIK+Y+PV++
Sbjct: 108 RQLELVEPSGWIHVPLTDNHKKPTRTFMIQIAVLANHQNGRDTHMRQIKIYTPVEE 163
Score = 94.4 bits (233), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 41/72 (56%), Positives = 55/72 (76%)
Query: 198 QVSVRAGTNFNDLQEIEVVDLNEPSGWVXXXXXXXXXXXXRTYMIQIAVMSNHQNGRDTH 257
++SVR G NF++LQEI ++L EPSGW+ RT+MIQIAV++NHQNGRDTH
Sbjct: 92 KISVRVGNNFHNLQEIRQLELVEPSGWIHVPLTDNHKKPTRTFMIQIAVLANHQNGRDTH 151
Query: 258 MRQIKVYSPVQQ 269
MRQIK+Y+PV++
Sbjct: 152 MRQIKIYTPVEE 163
>pdb|1GQP|A Chain A, Apc10DOC1 SUBUNIT OF S. CEREVISIAE
pdb|1GQP|B Chain B, Apc10DOC1 SUBUNIT OF S. CEREVISIAE
Length = 221
Score = 85.1 bits (209), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 52/167 (31%), Positives = 80/167 (47%), Gaps = 25/167 (14%)
Query: 18 GRIREVGSQAIWSLSSCKPGFGVDQLRDDCMDTYWQSDGQLPHLVNVQFRRKTTVQDICI 77
R+ V A+W SS K G VD DD DT+WQSDG PH +++ F ++ DIC+
Sbjct: 50 ARMINVTHLALWKPSSFKLGNPVDFALDDNYDTFWQSDGGQPHQLDIMFSKRM---DICV 106
Query: 78 YRQLPHLVNVQFRRKTTVQDICIYTDYKLDESYTPSRVSVRAGTNFNDLQEIEVVDLNEP 137
+ I+ DESY PS V V AG + +D + +++++
Sbjct: 107 --------------------MAIFFSMIADESYAPSLVKVYAGHSPSDARFYKMLEVRNV 146
Query: 138 SGWVXX--XXXXXXXXXXRTYMIQIAVMSNHQNGRDTHMRQIKVYSP 182
+GWV + I++ NH+NG+DTH+R I++Y P
Sbjct: 147 NGWVALRFLDNREDDQLLKCQFIRLLFPVNHENGKDTHLRGIRLYVP 193
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 199 VSVRAGTNFNDLQEIEVVDLNEPSGWVXXXXXXXXX--XXXRTYMIQIAVMSNHQNGRDT 256
V V AG + +D + +++++ +GWV + I++ NH+NG+DT
Sbjct: 124 VKVYAGHSPSDARFYKMLEVRNVNGWVALRFLDNREDDQLLKCQFIRLLFPVNHENGKDT 183
Query: 257 HMRQIKVYSP 266
H+R I++Y P
Sbjct: 184 HLRGIRLYVP 193
>pdb|1FS9|A Chain A, Cytochrome C Nitrite Reductase From Wolinella
Succinogenes-Azide Complex
Length = 507
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 32 SSCKPGFGVDQLRDDCMDTYWQSDGQLPHLVNVQFRRKTTVQDICI 77
S K G +D + CM+ + +S+ +L +V +F RK +QDI
Sbjct: 311 SDHKVGNPLDNMDKSCMNCHRESEQKLKDIVKQKFERKEFLQDIAF 356
>pdb|3BNG|A Chain A, W. Succinogenes Nrfa Y218f
pdb|3BNH|A Chain A, W. Succinogenes Nrfa Y218f Nitrite Complex
pdb|3BNJ|A Chain A, W. Succinogenes Nrfa Y218f Sulfite Complex
Length = 485
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 32 SSCKPGFGVDQLRDDCMDTYWQSDGQLPHLVNVQFRRKTTVQDICI 77
S K G +D + CM+ + +S+ +L +V +F RK +QDI
Sbjct: 289 SDHKVGNPLDNMDKSCMNCHRESEQKLKDIVKQKFERKEFLQDIAF 334
>pdb|1FS7|A Chain A, Cytochrome C Nitrite Reductase From Wolinella Succinogenes
pdb|1FS8|A Chain A, Cytochrome C Nitrite Reductase From Wolinella
Succinogenes-Sulfate Complex
pdb|2E80|A Chain A, Cytochrome C Nitrite Reductase From Wolinella Succinogenes
With Bound Substrate Nitrite
pdb|2E81|A Chain A, Cytochrome C Nitrite Reductase From Wolinella Succinogenes
With Bound Intermediate Hydroxylamine
pdb|3BNF|A Chain A, W. Succinogenes Nrfa Sulfite Complex
Length = 485
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 32 SSCKPGFGVDQLRDDCMDTYWQSDGQLPHLVNVQFRRKTTVQDICI 77
S K G +D + CM+ + +S+ +L +V +F RK +QDI
Sbjct: 289 SDHKVGNPLDNMDKSCMNCHRESEQKLKDIVKQKFERKEFLQDIAF 334
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 0.133 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,619,981
Number of Sequences: 62578
Number of extensions: 269605
Number of successful extensions: 726
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 716
Number of HSP's gapped (non-prelim): 7
length of query: 287
length of database: 14,973,337
effective HSP length: 98
effective length of query: 189
effective length of database: 8,840,693
effective search space: 1670890977
effective search space used: 1670890977
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: 51 (24.3 bits)