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= 039425
(413 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3EH2|A Chain A, Crystal Structure Of The Human Copii-Coat Protein Sec24c
pdb|3EH2|B Chain B, Crystal Structure Of The Human Copii-Coat Protein Sec24c
pdb|3EH2|C Chain C, Crystal Structure Of The Human Copii-Coat Protein Sec24c
Length = 766
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 12/65 (18%)
Query: 290 NSVMHFRNIKASLERSLTMVQHDFKLLIFKELRGFVATNALTMILDESRRV-----DSLG 344
N V+HF N+K+SL + MV D + L GF+ ++ESR V D +
Sbjct: 225 NKVLHFYNVKSSLAQPQMMVVSDVADMFVPLLDGFLVN------VNESRAVITSLLDQI- 277
Query: 345 PDVFA 349
P++FA
Sbjct: 278 PEMFA 282
>pdb|1VF5|A Chain A, Crystal Structure Of Cytochrome B6f Complex From
M.Laminosus
pdb|1VF5|N Chain N, Crystal Structure Of Cytochrome B6f Complex From
M.Laminosus
pdb|2D2C|A Chain A, Crystal Structure Of Cytochrome B6f Complex With Dbmib
From M. Laminosus
pdb|2D2C|N Chain N, Crystal Structure Of Cytochrome B6f Complex With Dbmib
From M. Laminosus
pdb|2E74|A Chain A, Crystal Structure Of The Cytochrome B6f Complex From
M.Laminosus
pdb|2E75|A Chain A, Crystal Structure Of The Cytochrome B6f Complex With
2-nonyl-4- Hydroxyquinoline N-oxide (nqno) From
M.laminosus
pdb|2E76|A Chain A, Crystal Structure Of The Cytochrome B6f Complex With
Tridecyl- Stigmatellin (Tds) From M.Laminosus
pdb|4H0L|A Chain A, Cytochrome B6f Complex Crystal Structure From
Mastigocladus Laminosus With N-side Inhibitor Nqno
pdb|4H13|A Chain A, Crystal Structure Of The Cytochrome B6f Complex From
Mastigocladus Laminosus With Tds
Length = 215
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 44/98 (44%), Gaps = 5/98 (5%)
Query: 129 YQTNRYDMP--LLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEENMLASVI 186
Y T + P L I+GV +T S L W+ WA++ + + E + V+
Sbjct: 105 YLTGGFKKPRELTWISGVILAVITVSFGVTGYSLPWDQVGYWAVKIVSGVPEAIPVVGVL 164
Query: 187 VTDRELALMTVIQK---HFPSATTFLCRWYISRNVLVN 221
++D +V Q + SA TF+ W I+ +L++
Sbjct: 165 ISDLLRGGSSVGQATLTRYYSAHTFVLPWLIAVFMLLH 202
>pdb|1U1W|A Chain A, Structure And Function Of Phenazine-biosynthesis Protein
Phzf From Pseudomonas Fluorescens 2-79
pdb|1U1W|B Chain B, Structure And Function Of Phenazine-biosynthesis Protein
Phzf From Pseudomonas Fluorescens 2-79
pdb|1U1X|A Chain A, Structure And Function Of Phenazine-Biosynthesis Protein
Phzf From Pseudomonas Fluorescens 2-79
pdb|1U1X|B Chain B, Structure And Function Of Phenazine-Biosynthesis Protein
Phzf From Pseudomonas Fluorescens 2-79
pdb|1XUA|A Chain A, Structure And Function Of The Phenazine Biosynthetic
Protein Phzf From Pseudomonas Fluorescens
pdb|1XUA|B Chain B, Structure And Function Of The Phenazine Biosynthetic
Protein Phzf From Pseudomonas Fluorescens
Length = 298
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 21/34 (61%)
Query: 378 VKRFNDSDDLAKVQLLRKLKELANPASTFLLEPK 411
V F D+DDL Q+ R +E+ STF+L+P+
Sbjct: 40 VAVFFDADDLPPAQMQRIAREMNLSESTFVLKPR 73
>pdb|1XUB|A Chain A, Structure And Function Of The Phenazine Biosynthetic
Protein Phzf From Pseudomonas Fluorescens
Length = 298
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 21/34 (61%)
Query: 378 VKRFNDSDDLAKVQLLRKLKELANPASTFLLEPK 411
V F D+DDL Q+ R +E+ STF+L+P+
Sbjct: 40 VAVFFDADDLPPAQMQRIAREMNLSESTFVLKPR 73
>pdb|1T6K|A Chain A, Crystal Structure Of Phzf From Pseudomonas Fluorescens
2-79
Length = 278
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 21/34 (61%)
Query: 378 VKRFNDSDDLAKVQLLRKLKELANPASTFLLEPK 411
V F D+DDL Q+ R +E+ STF+L+P+
Sbjct: 20 VAVFFDADDLPPAQMQRIAREMNLSESTFVLKPR 53
>pdb|2ZT9|A Chain A, Crystal Structure Of The Cytochrome B6f Complex From
Nostoc Sp. Pcc 7120
pdb|4H44|A Chain A, 2.70 A Cytochrome B6f Complex Structure From Nostoc Pcc
7120
Length = 215
Score = 29.6 bits (65), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 23/93 (24%), Positives = 40/93 (43%), Gaps = 5/93 (5%)
Query: 128 TYQTNRYDMP--LLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEENMLASV 185
Y T + P L ++GV +T S L W+ WA++ + + E + V
Sbjct: 104 VYLTGGFKKPRELTWVSGVILAVITVSFGVTGYSLPWDQVGYWAVKIVSGVPEAIPVVGV 163
Query: 186 IVTDRELALMTVIQK---HFPSATTFLCRWYIS 215
+++D +V Q + SA TF+ W I+
Sbjct: 164 LISDLLRGGSSVGQATLTRYYSAHTFVLPWLIA 196
>pdb|1Q0S|A Chain A, Binary Structure Of T4dam With Adohcy
pdb|1Q0T|A Chain A, Ternary Structure Of T4dam With Adohcy And Dna
pdb|1Q0T|B Chain B, Ternary Structure Of T4dam With Adohcy And Dna
Length = 259
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 30/63 (47%)
Query: 181 MLASVIVTDRELALMTVIQKHFPSATTFLCRWYISRNVLVNCKNLFEANEIWQTFISSWN 240
ML ++ T + +L+ ++ HFP F+ + +V +N AN+I + I +
Sbjct: 1 MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQEPIIEMYK 60
Query: 241 LLI 243
LI
Sbjct: 61 RLI 63
>pdb|1YFJ|A Chain A, T4dam In Complex With Adohcy And 15-Mer Oligonucleotide
Showing Semi-Specific And Specific Contact
pdb|1YFJ|B Chain B, T4dam In Complex With Adohcy And 15-Mer Oligonucleotide
Showing Semi-Specific And Specific Contact
pdb|1YFJ|C Chain C, T4dam In Complex With Adohcy And 15-Mer Oligonucleotide
Showing Semi-Specific And Specific Contact
pdb|1YFJ|D Chain D, T4dam In Complex With Adohcy And 15-Mer Oligonucleotide
Showing Semi-Specific And Specific Contact
pdb|1YFJ|E Chain E, T4dam In Complex With Adohcy And 15-Mer Oligonucleotide
Showing Semi-Specific And Specific Contact
pdb|1YFJ|F Chain F, T4dam In Complex With Adohcy And 15-Mer Oligonucleotide
Showing Semi-Specific And Specific Contact
pdb|1YFL|A Chain A, T4dam In Complex With Sinefungin And 16-Mer
Oligonucleotide Showing Semi-Specific And Specific
Contact And Flipped Base
pdb|1YFL|B Chain B, T4dam In Complex With Sinefungin And 16-Mer
Oligonucleotide Showing Semi-Specific And Specific
Contact And Flipped Base
pdb|1YFL|D Chain D, T4dam In Complex With Sinefungin And 16-Mer
Oligonucleotide Showing Semi-Specific And Specific
Contact And Flipped Base
pdb|1YFL|E Chain E, T4dam In Complex With Sinefungin And 16-Mer
Oligonucleotide Showing Semi-Specific And Specific
Contact And Flipped Base
Length = 259
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 30/63 (47%)
Query: 181 MLASVIVTDRELALMTVIQKHFPSATTFLCRWYISRNVLVNCKNLFEANEIWQTFISSWN 240
ML ++ T + +L+ ++ HFP F+ + +V +N AN+I + I +
Sbjct: 1 MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQEPIIEMYK 60
Query: 241 LLI 243
LI
Sbjct: 61 RLI 63
>pdb|1YF3|A Chain A, T4dam In Complex With Adohcy And 13-Mer Oligonucleotide
Making Non- And Semi-Specific (~14) CONTACT
pdb|1YF3|B Chain B, T4dam In Complex With Adohcy And 13-Mer Oligonucleotide
Making Non- And Semi-Specific (~14) CONTACT
Length = 259
Score = 28.9 bits (63), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 30/63 (47%)
Query: 181 MLASVIVTDRELALMTVIQKHFPSATTFLCRWYISRNVLVNCKNLFEANEIWQTFISSWN 240
ML ++ T + +L+ ++ HFP F+ + +V +N AN+I + I +
Sbjct: 1 MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQEPIIEMYK 60
Query: 241 LLI 243
LI
Sbjct: 61 RLI 63
>pdb|3DPL|C Chain C, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation
Length = 382
Score = 28.1 bits (61), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 84 LIEHKYIERHKSDVDT 99
LIEHKYI R +SD++T
Sbjct: 362 LIEHKYIRRDESDINT 377
>pdb|3DQV|C Chain C, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation
pdb|3DQV|D Chain D, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation
Length = 382
Score = 28.1 bits (61), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 84 LIEHKYIERHKSDVDT 99
LIEHKYI R +SD++T
Sbjct: 362 LIEHKYIRRDESDINT 377
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
0.323 0.135 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,184,677
Number of Sequences: 62578
Number of extensions: 417237
Number of successful extensions: 1153
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1144
Number of HSP's gapped (non-prelim): 13
length of query: 413
length of database: 14,973,337
effective HSP length: 101
effective length of query: 312
effective length of database: 8,652,959
effective search space: 2699723208
effective search space used: 2699723208
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)