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= 025604
(250 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2EXN|A Chain A, Solution Structure For The Protein Coded By Gene Locus
Bb0938 Of Bordetella Bronchiseptica. Northeast
Structural Genomics Target Bor11
Length = 136
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 35/131 (26%), Positives = 57/131 (43%), Gaps = 24/131 (18%)
Query: 14 PIKSCRGISVCQQAPLTPTGFRWDRQWMVINNNGRAYTQRNEPKLALVETELPNEAFLEG 73
PI C + + A + ++W+V N+ G+ + P+LA V EL
Sbjct: 8 PIAECGATTQSEAAA-------YQKRWLVANDAGQWLNRDLCPRLAEVSVEL-------- 52
Query: 74 WEPTGRSFMVIRAPGMQALKISLSKPRDIADGVS----VWEWCGSALAEGAEASNWFTNY 129
++V++APGM L I L D D V V E + EG A+ W +N+
Sbjct: 53 ----RMGYLVLKAPGMLRLDIPLDVIED-DDSVRYQMLVGEQTVDVVDEGELAAAWISNH 107
Query: 130 LGKPSRLVRYN 140
G P R+++ +
Sbjct: 108 AGVPCRILKVH 118
>pdb|3HOA|A Chain A, Crystal Structure Of The Thermus Thermophilus M32
Carboxypeptidase
pdb|3HOA|B Chain B, Crystal Structure Of The Thermus Thermophilus M32
Carboxypeptidase
Length = 509
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 40/148 (27%), Positives = 56/148 (37%), Gaps = 38/148 (25%)
Query: 53 RNEPKLALVETELPNEAFLEGWEPTGRSFMVIRAPGMQALKISLSKPRDIADGV-SVWEW 111
R E +LAL EL E E W R + + P+D DGV W
Sbjct: 373 RLELELALFRGELSPEDLPEAWAEKYRDHLGV-------------APKDYKDGVMQDVHW 419
Query: 112 CGSALAEGAEASNWFTNY-LGKPSRLVRYN-AESETRPVDPKYAAGEKIMFSDCYPFMLL 169
G +F Y LG + AE+E P++P++A GE F D +
Sbjct: 420 AGGLF-------GYFPTYTLGNLYAAQFFQKAEAELGPLEPRFARGEFQPFLDWTRARIH 472
Query: 170 SQGSLDALNKLLKEPIPINRFRPNILVD 197
++GS RFRP +LV+
Sbjct: 473 AEGS---------------RFRPRVLVE 485
>pdb|1WGZ|A Chain A, Crystal Structure Of Carboxypeptidase 1 From Thermus
Thermophilus
pdb|1WGZ|B Chain B, Crystal Structure Of Carboxypeptidase 1 From Thermus
Thermophilus
pdb|1WGZ|C Chain C, Crystal Structure Of Carboxypeptidase 1 From Thermus
Thermophilus
Length = 510
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 38/148 (25%), Positives = 55/148 (37%), Gaps = 38/148 (25%)
Query: 53 RNEPKLALVETELPNEAFLEGWEPTGRSFMVIRAPGMQALKISLSKPRDIADGV-SVWEW 111
R E +LAL EL E E W R + + P+D DGV W
Sbjct: 373 RLELELALFRGELSPEDLPEAWAEKYRDHLGV-------------APKDYKDGVMQDVHW 419
Query: 112 CGSALAEGAEASNWFTNYLGKPSRLVRY--NAESETRPVDPKYAAGEKIMFSDCYPFMLL 169
G +F Y ++ AE+E P++P++A GE F D +
Sbjct: 420 AGGLF-------GYFPTYTLGNLYAAQFFQKAEAELGPLEPRFARGEFQPFLDWTRARIH 472
Query: 170 SQGSLDALNKLLKEPIPINRFRPNILVD 197
++GS RFRP +LV+
Sbjct: 473 AEGS---------------RFRPRVLVE 485
>pdb|3NNE|A Chain A, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|B Chain B, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|C Chain C, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|D Chain D, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|E Chain E, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|F Chain F, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|G Chain G, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|H Chain H, Crystal Structure Of Choline Oxidase S101a Mutant
Length = 546
Score = 31.2 bits (69), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 36/83 (43%), Gaps = 10/83 (12%)
Query: 79 RSFMVIRAPGMQALKISLSKPRDIADGVSVWEWCGSALAEGAEA--SNWFTNYLGK---- 132
R F M+ + + K R+IA ++ EW G L+ G EA +Y+ K
Sbjct: 404 RYFTDPEGHDMRVMVAGIRKAREIAAQPAMAEWTGRELSPGVEAQTDEELQDYIRKTHNT 463
Query: 133 ---PSRLVRYNA-ESETRPVDPK 151
P VR A E E P+DP+
Sbjct: 464 VYHPVGTVRMGAVEDEMSPLDPE 486
>pdb|2JBV|A Chain A, Crystal Structure Of Choline Oxidase Reveals Insights Into
The Catalytic Mechanism
pdb|2JBV|B Chain B, Crystal Structure Of Choline Oxidase Reveals Insights Into
The Catalytic Mechanism
Length = 546
Score = 31.2 bits (69), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 36/83 (43%), Gaps = 10/83 (12%)
Query: 79 RSFMVIRAPGMQALKISLSKPRDIADGVSVWEWCGSALAEGAEA--SNWFTNYLGK---- 132
R F M+ + + K R+IA ++ EW G L+ G EA +Y+ K
Sbjct: 404 RYFTDPEGHDMRVMVAGIRKAREIAAQPAMAEWTGRELSPGVEAQTDEELQDYIRKTHNT 463
Query: 133 ---PSRLVRYNA-ESETRPVDPK 151
P VR A E E P+DP+
Sbjct: 464 VYHPVGTVRMGAVEDEMSPLDPE 486
>pdb|3LJP|A Chain A, Crystal Structure Of Choline Oxidase V464a Mutant
pdb|3LJP|B Chain B, Crystal Structure Of Choline Oxidase V464a Mutant
Length = 546
Score = 31.2 bits (69), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 36/83 (43%), Gaps = 10/83 (12%)
Query: 79 RSFMVIRAPGMQALKISLSKPRDIADGVSVWEWCGSALAEGAEA--SNWFTNYLGK---- 132
R F M+ + + K R+IA ++ EW G L+ G EA +Y+ K
Sbjct: 404 RYFTDPEGHDMRVMVAGIRKAREIAAQPAMAEWTGRELSPGVEAQTDEELQDYIRKTHNT 463
Query: 133 ---PSRLVRYNA-ESETRPVDPK 151
P VR A E E P+DP+
Sbjct: 464 AYHPVGTVRMGAVEDEMSPLDPE 486
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 0.136 0.434
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,441,202
Number of Sequences: 62578
Number of extensions: 295754
Number of successful extensions: 673
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 672
Number of HSP's gapped (non-prelim): 6
length of query: 250
length of database: 14,973,337
effective HSP length: 96
effective length of query: 154
effective length of database: 8,965,849
effective search space: 1380740746
effective search space used: 1380740746
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: 50 (23.9 bits)