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= psy12048
(267 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1RK8|C Chain C, Structure Of The Cytosolic Protein Pym Bound To The
Mago- Y14 Core Of The Exon Junction Complex
Length = 58
Score = 68.9 bits (167), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 34/47 (72%), Positives = 39/47 (82%), Gaps = 1/47 (2%)
Query: 2 GVYIQPSRRPDGTFRKAIRVKAGYVPQDEVPLYESKGKQF-ANRQAA 47
G +I ++RPDGT+RKA RVK GYVPQ+EVPLYESKGKQF A RQA
Sbjct: 10 GKFIPATKRPDGTWRKARRVKDGYVPQEEVPLYESKGKQFVAQRQAG 56
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/25 (84%), Positives = 22/25 (88%), Gaps = 1/25 (4%)
Query: 81 GYVPQDEVPLYESKGKQF-ANRQAA 104
GYVPQ+EVPLYESKGKQF A RQA
Sbjct: 32 GYVPQEEVPLYESKGKQFVAQRQAG 56
>pdb|3VBA|A Chain A, Crystal Structure Of Methanogen 3-Isopropylmalate
Isomerase Small Subunit
pdb|3VBA|B Chain B, Crystal Structure Of Methanogen 3-Isopropylmalate
Isomerase Small Subunit
pdb|3VBA|C Chain C, Crystal Structure Of Methanogen 3-Isopropylmalate
Isomerase Small Subunit
pdb|3VBA|D Chain D, Crystal Structure Of Methanogen 3-Isopropylmalate
Isomerase Small Subunit
pdb|3VBA|E Chain E, Crystal Structure Of Methanogen 3-Isopropylmalate
Isomerase Small Subunit
pdb|3VBA|F Chain F, Crystal Structure Of Methanogen 3-Isopropylmalate
Isomerase Small Subunit
Length = 176
Score = 33.9 bits (76), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 27/45 (60%)
Query: 202 IKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRKPDLLSEIM 246
K + +KV E LE +E+GEIKN ++ K Q+ P+ + EI+
Sbjct: 107 CKGISEKVNEGDELEVNLETGEIKNLTTGEVLKGQKLPEFMMEIL 151
>pdb|1Z8S|A Chain A, Dnab Binding Domain Of Dnag (P16) From Bacillus
Stearothermophilus (Residues 452-597)
Length = 146
Score = 30.8 bits (68), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 36/144 (25%), Positives = 60/144 (41%), Gaps = 28/144 (19%)
Query: 74 ILDADDLGYVPQDEVPLYESKGKQF---ANRQAAQSIPIGLDPSHVKKPVNPQNPIPG-L 129
++ + D+ V Q+ + G +F +R A I + H P + IPG L
Sbjct: 20 MMRSRDVALVVQERI------GGRFNIEEHRALAAYIYAFYEEGHEADPGALISRIPGEL 73
Query: 130 PPAPSELNF----DNLSPEELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAP 185
P SEL+ D++S +ELE I+ H + P+ L LKV +
Sbjct: 74 QPLASELSLLLIADDVSEQELEDYIR--------------HVLNRPKWLMLKVKEQEKTE 119
Query: 186 SELNFDNLSPEELEKRIKNLKKKV 209
+E D L+ + K + +KK +
Sbjct: 120 AERRKDFLTAARIAKEMIEMKKML 143
>pdb|2D0V|B Chain B, Crystal Structure Of Methanol Dehydrogenase From
Hyphomicrobium Denitrificans
pdb|2D0V|E Chain E, Crystal Structure Of Methanol Dehydrogenase From
Hyphomicrobium Denitrificans
pdb|2D0V|J Chain J, Crystal Structure Of Methanol Dehydrogenase From
Hyphomicrobium Denitrificans
Length = 72
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 111 LDPSHVKKPVNPQNPIPGLPPAPSELNFD-NLSPEELEKRIKNLK 154
D +H K P N P PG P + +D P+EL K++++ K
Sbjct: 1 YDGTHCKAPGNCWEPKPGFPEKIAGSKYDPKHDPKELNKQVESRK 45
>pdb|1OJ6|A Chain A, Human Brain Neuroglobin Three-Dimensional Structure
pdb|1OJ6|B Chain B, Human Brain Neuroglobin Three-Dimensional Structure
pdb|1OJ6|C Chain C, Human Brain Neuroglobin Three-Dimensional Structure
pdb|1OJ6|D Chain D, Human Brain Neuroglobin Three-Dimensional Structure
Length = 151
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 44/80 (55%), Gaps = 12/80 (15%)
Query: 86 DEVPLYESKGKQFANRQAAQSIPIGLDPSHVKKPVNPQNPIPGLPPAPSELNFDNLSPEE 145
D +PL++ G+QF++ + + S P LD H++K + L + N ++LS
Sbjct: 37 DLLPLFQYNGRQFSSPEDSLSSPEFLD--HIRKVM--------LVIDAAVTNVEDLS--S 84
Query: 146 LEKRIKNLKKKVREITVQVT 165
LE+ + +L +K R + V+++
Sbjct: 85 LEEYLASLGRKHRAVGVKLS 104
>pdb|3IR5|A Chain A, Crystal Structure Of Narghi Mutant Narg-H49c
Length = 1247
Score = 28.1 bits (61), Expect = 5.3, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 21/44 (47%)
Query: 68 PIPGLVILDADDLGYVPQDEVPLYESKGKQFANRQAAQSIPIGL 111
P+ L DA DLG D + ++ S G A +Q +P G+
Sbjct: 1116 PVVWLSEADAKDLGIADNDWIEVFNSNGALTARAVVSQRVPAGM 1159
>pdb|1R27|A Chain A, Crystal Structure Of Nargh Complex
pdb|1R27|C Chain C, Crystal Structure Of Nargh Complex
pdb|1SIW|A Chain A, Crystal Structure Of The Apomolybdo-Narghi
pdb|1Y4Z|A Chain A, The Crystal Structure Of Nitrate Reductase A, Narghi, In
Complex With The Q-Site Inhibitor Pentachlorophenol
pdb|1Y5I|A Chain A, The Crystal Structure Of The Narghi Mutant Nari-K86a
pdb|1Y5L|A Chain A, The Crystal Structure Of The Narghi Mutant Nari-H66y
pdb|1Y5N|A Chain A, The Crystal Structure Of The Narghi Mutant Nari-K86a In
Complex With Pentachlorophenol
Length = 1246
Score = 28.1 bits (61), Expect = 5.4, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 21/44 (47%)
Query: 68 PIPGLVILDADDLGYVPQDEVPLYESKGKQFANRQAAQSIPIGL 111
P+ L DA DLG D + ++ S G A +Q +P G+
Sbjct: 1115 PVVWLSEADAKDLGIADNDWIEVFNSNGALTARAVVSQRVPAGM 1158
>pdb|3EGW|A Chain A, The Crystal Structure Of The Narghi Mutant Narh - C16a
Length = 1244
Score = 28.1 bits (61), Expect = 5.4, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 21/44 (47%)
Query: 68 PIPGLVILDADDLGYVPQDEVPLYESKGKQFANRQAAQSIPIGL 111
P+ L DA DLG D + ++ S G A +Q +P G+
Sbjct: 1115 PVVWLSEADAKDLGIADNDWIEVFNSNGALTARAVVSQRVPAGM 1158
>pdb|3IR7|A Chain A, Crystal Structure Of Narghi Mutant Narg-R94s
Length = 1247
Score = 28.1 bits (61), Expect = 5.4, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 21/44 (47%)
Query: 68 PIPGLVILDADDLGYVPQDEVPLYESKGKQFANRQAAQSIPIGL 111
P+ L DA DLG D + ++ S G A +Q +P G+
Sbjct: 1116 PVVWLSEADAKDLGIADNDWIEVFNSNGALTARAVVSQRVPAGM 1159
>pdb|3IR6|A Chain A, Crystal Structure Of Narghi Mutant Narg-H49s
Length = 1247
Score = 28.1 bits (61), Expect = 5.4, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 21/44 (47%)
Query: 68 PIPGLVILDADDLGYVPQDEVPLYESKGKQFANRQAAQSIPIGL 111
P+ L DA DLG D + ++ S G A +Q +P G+
Sbjct: 1116 PVVWLSEADAKDLGIADNDWIEVFNSNGALTARAVVSQRVPAGM 1159
>pdb|1Q16|A Chain A, Crystal Structure Of Nitrate Reductase A, Narghi, From
Escherichia Coli
Length = 1247
Score = 28.1 bits (61), Expect = 5.4, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 21/44 (47%)
Query: 68 PIPGLVILDADDLGYVPQDEVPLYESKGKQFANRQAAQSIPIGL 111
P+ L DA DLG D + ++ S G A +Q +P G+
Sbjct: 1116 PVVWLSEADAKDLGIADNDWIEVFNSNGALTARAVVSQRVPAGM 1159
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
0.311 0.133 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,140,328
Number of Sequences: 62578
Number of extensions: 356558
Number of successful extensions: 1162
Number of sequences better than 100.0: 48
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 1130
Number of HSP's gapped (non-prelim): 58
length of query: 267
length of database: 14,973,337
effective HSP length: 97
effective length of query: 170
effective length of database: 8,903,271
effective search space: 1513556070
effective search space used: 1513556070
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 50 (23.9 bits)