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= 046883
(292 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1N7Z|A Chain A, Structure And Location Of Gene Product 8 In The
Bacteriophage T4 Baseplate
pdb|1N7Z|B Chain B, Structure And Location Of Gene Product 8 In The
Bacteriophage T4 Baseplate
pdb|1N7Z|C Chain C, Structure And Location Of Gene Product 8 In The
Bacteriophage T4 Baseplate
pdb|1N7Z|D Chain D, Structure And Location Of Gene Product 8 In The
Bacteriophage T4 Baseplate
Length = 334
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 23/49 (46%), Gaps = 10/49 (20%)
Query: 108 TAFALEDNEFWPRHLFGFIFQVVA----------AVYVFLLTLPGNKLF 146
T + EDN W + FG I++V A +VY LPGNK F
Sbjct: 221 TRWGYEDNLTWQQDDFGLIYRVKANTIRFKAYLDSVYFPEAALPGNKGF 269
>pdb|1N80|A Chain A, Bacteriophage T4 Baseplate Structural Protein Gp8
pdb|1N80|B Chain B, Bacteriophage T4 Baseplate Structural Protein Gp8
pdb|1N80|C Chain C, Bacteriophage T4 Baseplate Structural Protein Gp8
pdb|1N80|D Chain D, Bacteriophage T4 Baseplate Structural Protein Gp8
pdb|1N8B|A Chain A, Bacteriophage T4 Baseplate Structural Protein Gp8
pdb|1N8B|B Chain B, Bacteriophage T4 Baseplate Structural Protein Gp8
pdb|1N8B|C Chain C, Bacteriophage T4 Baseplate Structural Protein Gp8
pdb|1N8B|D Chain D, Bacteriophage T4 Baseplate Structural Protein Gp8
pdb|1PDM|A Chain A, Fitting Of Gp8 Structure Into The Cryoem Reconstruction Of
The Bacteriophage T4 Baseplate
pdb|1PDM|B Chain B, Fitting Of Gp8 Structure Into The Cryoem Reconstruction Of
The Bacteriophage T4 Baseplate
pdb|1PDM|C Chain C, Fitting Of Gp8 Structure Into The Cryoem Reconstruction Of
The Bacteriophage T4 Baseplate
pdb|1PDM|D Chain D, Fitting Of Gp8 Structure Into The Cryoem Reconstruction Of
The Bacteriophage T4 Baseplate
pdb|1PDM|E Chain E, Fitting Of Gp8 Structure Into The Cryoem Reconstruction Of
The Bacteriophage T4 Baseplate
pdb|1PDM|F Chain F, Fitting Of Gp8 Structure Into The Cryoem Reconstruction Of
The Bacteriophage T4 Baseplate
pdb|1PDM|G Chain G, Fitting Of Gp8 Structure Into The Cryoem Reconstruction Of
The Bacteriophage T4 Baseplate
pdb|1PDM|H Chain H, Fitting Of Gp8 Structure Into The Cryoem Reconstruction Of
The Bacteriophage T4 Baseplate
pdb|1PDM|I Chain I, Fitting Of Gp8 Structure Into The Cryoem Reconstruction Of
The Bacteriophage T4 Baseplate
pdb|1PDM|J Chain J, Fitting Of Gp8 Structure Into The Cryoem Reconstruction Of
The Bacteriophage T4 Baseplate
pdb|1PDM|K Chain K, Fitting Of Gp8 Structure Into The Cryoem Reconstruction Of
The Bacteriophage T4 Baseplate
pdb|1PDM|L Chain L, Fitting Of Gp8 Structure Into The Cryoem Reconstruction Of
The Bacteriophage T4 Baseplate
pdb|1TJA|A Chain A, Fitting Of Gp8, Gp9, And Gp11 Into The Cryo-em
Reconstruction Of The Bacteriophage T4 Contracted Tail
pdb|1TJA|B Chain B, Fitting Of Gp8, Gp9, And Gp11 Into The Cryo-em
Reconstruction Of The Bacteriophage T4 Contracted Tail
Length = 334
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 23/49 (46%), Gaps = 10/49 (20%)
Query: 108 TAFALEDNEFWPRHLFGFIFQVVA----------AVYVFLLTLPGNKLF 146
T + EDN W + FG I++V A +VY LPGNK F
Sbjct: 221 TRWGYEDNLTWQQDDFGLIYRVKANTIRFKAYLDSVYFPEAALPGNKGF 269
>pdb|3VN9|A Chain A, Rifined Crystal Structure Of Non-Phosphorylated Map2k6 In
A Putative Auto-Inhibition State
Length = 340
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 31/122 (25%), Positives = 53/122 (43%), Gaps = 23/122 (18%)
Query: 156 GVIKYFERILALYLASVEKFRDSTLRELAEHYQKRDIVIKKDRCYLEVGCQYFKIFKG-- 213
GV++ + + + +V++ R + + QKR +++ D V C + F G
Sbjct: 65 GVVEKMRHVPSGQIMAVKRIRAT----VNSQEQKR-LLMDLDISMRTVDCPFTVTFYGAL 119
Query: 214 -------ILLELMSN-----FKRVNFAGPFFRDFSPEDVLGIIEVELNLVYEVLYTKIQV 261
I +ELM +K+V G PED+LG I V + E L++K+ V
Sbjct: 120 FREGDVWICMELMDTSLDKFYKQVIDKGQTI----PEDILGKIAVSIVKALEHLHSKLSV 175
Query: 262 TH 263
H
Sbjct: 176 IH 177
>pdb|3FME|A Chain A, Crystal Structure Of Human Mitogen-Activated Protein
Kinase Kinase 6 (Mek6) Activated Mutant (S207d, T211d)
Length = 290
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 31/122 (25%), Positives = 53/122 (43%), Gaps = 23/122 (18%)
Query: 156 GVIKYFERILALYLASVEKFRDSTLRELAEHYQKRDIVIKKDRCYLEVGCQYFKIFKG-- 213
GV++ + + + +V++ R + + QKR +++ D V C + F G
Sbjct: 21 GVVEKMRHVPSGQIMAVKRIRAT----VNSQEQKR-LLMDLDISMRTVDCPFTVTFYGAL 75
Query: 214 -------ILLELMSN-----FKRVNFAGPFFRDFSPEDVLGIIEVELNLVYEVLYTKIQV 261
I +ELM +K+V G PED+LG I V + E L++K+ V
Sbjct: 76 FREGDVWICMELMDTSLDKFYKQVIDKGQTI----PEDILGKIAVSIVKALEHLHSKLSV 131
Query: 262 TH 263
H
Sbjct: 132 IH 133
>pdb|4DJH|A Chain A, Structure Of The Human Kappa Opioid Receptor In Complex
With Jdtic
pdb|4DJH|B Chain B, Structure Of The Human Kappa Opioid Receptor In Complex
With Jdtic
Length = 480
Score = 28.1 bits (61), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 28/119 (23%), Positives = 47/119 (39%), Gaps = 4/119 (3%)
Query: 108 TAFALEDNEFWPRHLFGFIFQVVAAVY--VFLLTLPGNKLFIPTILMFIAGVIKYFERIL 165
T ED + P H+ I ++ AVY VF++ L GN L + I+ + +K I
Sbjct: 3 TTMGSEDAQLEPAHISPAIPVIITAVYSVVFVVGLVGNSLVMFVIIRYTK--MKTATNIY 60
Query: 166 ALYLASVEKFRDSTLRELAEHYQKRDIVIKKDRCYLEVGCQYFKIFKGILLELMSNFKR 224
LA + +T+ + Y C + + Y+ +F I M + R
Sbjct: 61 IFNLALADALVTTTMPFQSTVYLMNSWPFGDVLCKIVLSIDYYNMFTSIFTLTMMSVDR 119
>pdb|1PYY|A Chain A, Double Mutant Pbp2x T338aM339F FROM STREPTOCOCCUS
PNEUMONIAE STRAIN R6 At 2.4 A Resolution
Length = 702
Score = 27.7 bits (60), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 41 GTGNKLVISVVWSAYLLADWVVNFGVGLITERARDTPDHSKQPAENNELLAFWVPFLLSH 100
GTG K+ S LA N V +++++A + PD E E LA W+ L
Sbjct: 616 GTGTKIKNSSAEEGKNLA---PNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEF 672
Query: 101 LGSPDTI 107
GS T+
Sbjct: 673 QGSGSTV 679
>pdb|1QME|A Chain A, Penicillin-binding Protein 2x (pbp-2x)
pdb|1QMF|A Chain A, Penicillin-Binding Protein 2x (Pbp-2x) Acyl-Enzyme Complex
Length = 702
Score = 27.7 bits (60), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 41 GTGNKLVISVVWSAYLLADWVVNFGVGLITERARDTPDHSKQPAENNELLAFWVPFLLSH 100
GTG K+ S LA N V +++++A + PD E E LA W+ L
Sbjct: 616 GTGTKIKNSSAEEGKNLA---PNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEF 672
Query: 101 LGSPDTI 107
GS T+
Sbjct: 673 QGSGSTV 679
>pdb|1PMD|A Chain A, Penicillin-Binding Protein 2x (Pbp-2x)
Length = 675
Score = 27.7 bits (60), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 41 GTGNKLVISVVWSAYLLADWVVNFGVGLITERARDTPDHSKQPAENNELLAFWVPFLLSH 100
GTG K+ S LA N V +++++A + PD E E LA W+ L
Sbjct: 589 GTGTKIKNSSAEEGKNLA---PNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEF 645
Query: 101 LGSPDTI 107
GS T+
Sbjct: 646 QGSGSTV 652
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
0.329 0.145 0.445
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,540,893
Number of Sequences: 62578
Number of extensions: 350760
Number of successful extensions: 854
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 854
Number of HSP's gapped (non-prelim): 9
length of query: 292
length of database: 14,973,337
effective HSP length: 98
effective length of query: 194
effective length of database: 8,840,693
effective search space: 1715094442
effective search space used: 1715094442
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 bits)