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= psy13868
(128 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1OJ7|A Chain A, Structural Genomics, Unknown Function Crystal Structure Of
E. Coli K-12 Yqhd
pdb|1OJ7|B Chain B, Structural Genomics, Unknown Function Crystal Structure Of
E. Coli K-12 Yqhd
pdb|1OJ7|C Chain C, Structural Genomics, Unknown Function Crystal Structure Of
E. Coli K-12 Yqhd
pdb|1OJ7|D Chain D, Structural Genomics, Unknown Function Crystal Structure Of
E. Coli K-12 Yqhd
Length = 408
Score = 28.5 bits (62), Expect = 1.2, Method: Composition-based stats.
Identities = 26/111 (23%), Positives = 45/111 (40%), Gaps = 20/111 (18%)
Query: 32 GAVVWYTDGSKTEAGSGAGIHC--VKPRVNISLPLGTYT--------GVYQAEVLAIRNC 81
GAV+ S+ G H V+P + P+ TYT GV A V +
Sbjct: 170 GAVI-----SRKTTGDKQAFHSAHVQPVFAVLDPVYTYTLPPRQVANGVVDAFVHTVEQY 224
Query: 82 AEENINMGLSKR-----EIYIFSDSQAALRAIGNFQTKSKITWESTQAICG 127
+ ++ + R + + D AL+ N+ ++ + W +TQA+ G
Sbjct: 225 VTKPVDAKIHDRFAEGILLTLIEDGPKALKEPENYDVRANVMWAATQALNG 275
>pdb|3SK3|A Chain A, Crystal Structure Of Salmonella Typhimurium Acetate
Kinase (Acka) With Citrate Bound At The Dimeric
Interface
pdb|3SK3|B Chain B, Crystal Structure Of Salmonella Typhimurium Acetate
Kinase (Acka) With Citrate Bound At The Dimeric
Interface
pdb|3SLC|A Chain A, Crystal Structure Of Apo Form Of Acetate Kinase (Acka)
From Salmonella Typhimurium
pdb|3SLC|B Chain B, Crystal Structure Of Apo Form Of Acetate Kinase (Acka)
From Salmonella Typhimurium
pdb|3SLC|C Chain C, Crystal Structure Of Apo Form Of Acetate Kinase (Acka)
From Salmonella Typhimurium
pdb|3SLC|D Chain D, Crystal Structure Of Apo Form Of Acetate Kinase (Acka)
From Salmonella Typhimurium
Length = 415
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 22 GVKETQLLKKGAVVWYTDGSKTEAGSGAG 50
G+ E L + + W DGSK EA GAG
Sbjct: 47 GLAECFHLPEARIKWKMDGSKQEAALGAG 75
>pdb|3BBO|X Chain X, Homology Model For The Spinach Chloroplast 50s Subunit
Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
Length = 198
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 25/65 (38%), Gaps = 18/65 (27%)
Query: 5 ENFDNPVNVVIETAGNWGVKET------------------QLLKKGAVVWYTDGSKTEAG 46
EN P+ + IE+A G T Q+ K GA++ G+K AG
Sbjct: 46 ENLQAPIPLTIESAHKKGAGSTKNGRDSPGQRLGVKIYGDQVAKPGAIIVRQRGTKFHAG 105
Query: 47 SGAGI 51
GI
Sbjct: 106 KNVGI 110
>pdb|2G8F|A Chain A, B. Halodurans Rnase H Catalytic Domain E188a Mutant In
Complex With Mg2+ And RnaDNA HYBRID (NON-P Nick At The
Active Site)
pdb|2G8V|A Chain A, B. Halodurans Rnase H Catalytic Domain E188a Mutant In
Complex With Mg2+ And Rna/dna Hybrid (reaction Product)
pdb|2G8W|A Chain A, B. Halodurans Rnase H Catalytic Domain E188a Mutant In
Complex With Ca2+ And RnaDNA HYBRID
Length = 142
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 8/57 (14%)
Query: 62 LPLGTYT-GVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIGNFQTKSKI 117
+P+GT G + A V +R E N S++ IY SDSQ A++ + + + KS +
Sbjct: 46 IPIGTNNMGEFLAIVHGLRYLKERN-----SRKPIY--SDSQTAIKWVKDKKAKSTL 95
>pdb|2LHF|A Chain A, Solution Structure Of Outer Membrane Protein H (Oprh)
From P. Aeruginosa In Dhpc Micelles
Length = 179
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 2 AVEENFDNP-VNVVIETAGNWGVKETQLLKKGA-VVWYTDGSKTEAGSGAGIHCVKPRVN 59
++ N ++P ++ VI+ G WG++ Q ++G Y + S T +G+ + +
Sbjct: 21 SLNRNLNSPNLDKVIDNTGTWGIRAGQQFEQGRYYATYENISDTSSGNKLRQQNLLGSYD 80
Query: 60 ISLPLG 65
LP+G
Sbjct: 81 AFLPIG 86
>pdb|1ZBL|A Chain A, Bacillus Halodurans Rnase H Catalytic Domain Mutant D192n
In Complex With 12-Mer RnaDNA HYBRID
pdb|1ZBL|B Chain B, Bacillus Halodurans Rnase H Catalytic Domain Mutant D192n
In Complex With 12-Mer RnaDNA HYBRID
Length = 139
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 8/57 (14%)
Query: 62 LPLGTYT-GVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIGNFQTKSKI 117
+P+GT G + A V +R E N S++ IY SDSQ A++ + + + KS +
Sbjct: 46 IPIGTNNMGEFLAIVHGLRYLKERN-----SRKPIY--SDSQTAIKWVKDKKAKSTL 95
>pdb|2G8H|A Chain A, B. Halodurans Rnase H Catalytic Domain D192n Mutant In
Complex With Mg2+ And RnaDNA HYBRID (NON-P Nick At The
Active Site)
pdb|2G8I|A Chain A, B. Halodurans Rnase H Catalytic Domain D192n Mutant In
Complex With Mn2+ And RnaDNA HYBRID (NON-P Nick At The
Active Site)
pdb|2G8K|A Chain A, B. Halodurans Rnase H Catalytic Domain D192n Mutant In
Complex With Ca2+ And RnaDNA HYBRID (NON-P Nick At The
Active Site)
Length = 142
Score = 26.2 bits (56), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 8/57 (14%)
Query: 62 LPLGTYT-GVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIGNFQTKSKI 117
+P+GT G + A V +R E N S++ IY SDSQ A++ + + + KS +
Sbjct: 46 IPIGTNNMGEFLAIVHGLRYLKERN-----SRKPIY--SDSQTAIKWVKDKKAKSTL 95
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
0.314 0.131 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,748,180
Number of Sequences: 62578
Number of extensions: 144408
Number of successful extensions: 239
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 237
Number of HSP's gapped (non-prelim): 8
length of query: 128
length of database: 14,973,337
effective HSP length: 87
effective length of query: 41
effective length of database: 9,529,051
effective search space: 390691091
effective search space used: 390691091
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 45 (21.9 bits)