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= 039261
(182 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2LM4|A Chain A, Solution Nmr Structure Of Mitochondrial Succinate
Dehydrogenase Assembly Factor 2 From Saccharomyces
Cerevisiae, Northeast Structural Genomics Consortium
Target Yt682a
Length = 109
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 39/67 (58%), Gaps = 6/67 (8%)
Query: 69 RLLYRSKQRGFLELDLVLGKWVEEHIHSMDENGIKALVDVLNLENPDLWKWLTGQEQPPE 128
RL+Y+S++RG LE DL+L + +++ M+E ++ +LN + D++ W T
Sbjct: 25 RLIYQSRKRGILETDLLLSGFAAKYLKKMNEEELEEYDSLLNELDWDIYYWATKN----- 79
Query: 129 AVKTNPV 135
KT+P+
Sbjct: 80 -FKTSPL 85
>pdb|2JR5|A Chain A, Solution Structure Of Upf0350 Protein Vc_2471. Northeast
Structural Genomics Target Vcr36
Length = 94
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 74 SKQRGFLELDLVLGKWVEEHIHSMDENGIKALVDVLNLENPDLWKWLTGQ 123
+ +RG LELD+V+ + EE S+ E+ V +L ++PDL+ W+ G
Sbjct: 13 ACRRGMLELDVVIMPFFEECFDSLTESEQDDFVALLESDDPDLFAWVMGH 62
>pdb|1X6I|A Chain A, Crystal Structure Of Ygfy From Escherichia Coli
pdb|1X6I|B Chain B, Crystal Structure Of Ygfy From Escherichia Coli
pdb|1X6J|A Chain A, Crystal Structure Of Ygfy From Escherichia Coli
Length = 91
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 31/56 (55%)
Query: 74 SKQRGFLELDLVLGKWVEEHIHSMDENGIKALVDVLNLENPDLWKWLTGQEQPPEA 129
+ +RG ELD+ + + E S+ ++ + + +L ++PDL+ WL +P +A
Sbjct: 15 ACRRGMRELDISIMPFFEHEYDSLSDDEKRIFIRLLECDDPDLFNWLMNHGKPADA 70
>pdb|1PUZ|A Chain A, Solution Nmr Structure Of Protein Nma1147 From Neisseria
Meningitidis. Northeast Structural Genomics Consortium
Target Mr19
Length = 82
Score = 34.3 bits (77), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 12/51 (23%), Positives = 28/51 (54%)
Query: 76 QRGFLELDLVLGKWVEEHIHSMDENGIKALVDVLNLENPDLWKWLTGQEQP 126
+RG LELDL+ G+++E+ + + + ++L ++ +L + G +
Sbjct: 17 RRGLLELDLIFGRFMEKEFEHLSDKELSEFSEILEFQDQELLALINGHSET 67
>pdb|4AF5|A Chain A, Structure Of The C. Glutamicum Acnr Crystal Form I
Length = 190
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 29/44 (65%), Gaps = 5/44 (11%)
Query: 97 MDENGIKALVDVLN--LENPDLWKWLTGQEQPPEAVKTNPVFSA 138
+ ENG LV+V+ LE+P+ + W++ + + + ++T+PVF A
Sbjct: 76 VSENG---LVEVMRGMLEDPERYDWMSVRLEISKQLRTDPVFRA 116
>pdb|4AC6|A Chain A, Corynebacterium Glutamicum Acnr Au Derivative Structure
pdb|4ACI|A Chain A, Structure Of The C. Glutamicum Acnr Crystal Form Ii
pdb|4ACI|B Chain B, Structure Of The C. Glutamicum Acnr Crystal Form Ii
Length = 191
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 29/44 (65%), Gaps = 5/44 (11%)
Query: 97 MDENGIKALVDVLN--LENPDLWKWLTGQEQPPEAVKTNPVFSA 138
+ ENG LV+V+ LE+P+ + W++ + + + ++T+PVF A
Sbjct: 77 VSENG---LVEVMRGMLEDPERYDWMSVRLEISKQLRTDPVFRA 117
>pdb|3UQ2|A Chain A, Crystal Structure Of The Post-Catalytic Product Complex Of
Polymerase Lambda With An Rcmp Inserted Opposite A
Templating G And Damp Inserted Opposite A Templating T
At The Primer Terminus.
pdb|4FO6|A Chain A, Crystal Structure Of The Pre-Catalytic Ternary Complex Of
Polymerase Lambda With A Datp Analog Opposite A
Templating T And An Rcmp At The Primer Terminus
Length = 329
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 2/48 (4%)
Query: 43 YRWVSNTTQSLDIDLSNDEKK--KRLFNRLLYRSKQRGFLELDLVLGK 88
YR T +D+ +++ + + + +F+RLL +Q GFL DLV G+
Sbjct: 177 YRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVKGE 224
>pdb|3MGH|A Chain A, Binary Complex Of A Dna Polymerase Lambda Loop Mutant
pdb|3MGH|C Chain C, Binary Complex Of A Dna Polymerase Lambda Loop Mutant
pdb|3MGI|A Chain A, Ternary Complex Of A Dna Polymerase Lambda Loop Mutant
pdb|3PML|A Chain A, Crystal Structure Of A Polymerase Lambda Variant With A
Dgtp Analog Opposite A Templating T
pdb|3PML|B Chain B, Crystal Structure Of A Polymerase Lambda Variant With A
Dgtp Analog Opposite A Templating T
pdb|3PMN|A Chain A, Ternary Crystal Structure Of Polymerase Lambda Variant
With A Gt Mispair At The Primer Terminus With Mn2+ In
The Active Site
pdb|3PNC|A Chain A, Ternary Crystal Structure Of A Polymerase Lambda Variant
With A Gt Mispair At The Primer Terminus And Sodium At
Catalytic Metal Site
pdb|3UPQ|A Chain A, Crystal Structure Of The Pre-Catalytic Ternary Complex Of
Polymerase Lambda With An Ratp Analog Opposite A
Templating T.
pdb|3UQ0|A Chain A, Crystal Structure Of The Post-Catalytic Product Complex Of
Polymerase Lambda With An Ramp At The Primer Terminus
Length = 329
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 2/48 (4%)
Query: 43 YRWVSNTTQSLDIDLSNDEKK--KRLFNRLLYRSKQRGFLELDLVLGK 88
YR T +D+ +++ + + + +F+RLL +Q GFL DLV G+
Sbjct: 177 YRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVKGE 224
>pdb|3MZY|A Chain A, The Crystal Structure Of The Rna Polymerase Sigma-H Factor
F Fusobacterium Nucleatum To 2.5a
Length = 164
Score = 27.7 bits (60), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 128 EAVKTNPVF--SALHNKVMNNLNSYASPETRSEPGQPWVRGWDDFKKGRDSPLS 179
EA+KTN + SA + +N+N+Y S E+ E ++FKK ++ S
Sbjct: 58 EALKTNAILEDSAYFDDEGHNINNYKSSESNPEEAYLLKEEIEEFKKFSENNFS 111
>pdb|1BII|A Chain A, The Crystal Structure Of H-2dd Mhc Class I In Complex With
The Hiv-1 Derived Peptide P18-110
Length = 365
Score = 26.9 bits (58), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 2/57 (3%)
Query: 83 DLVLGKWVEEHIHSMDENGIKALVDVLNLENPDLWKWLTGQEQPPEAVKTNPVFSAL 139
D KW + E V+ L P +W G+E+PP + KTN V A+
Sbjct: 262 DGTFQKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRW--GKEEPPSSTKTNTVIIAV 316
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
0.316 0.133 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,364,382
Number of Sequences: 62578
Number of extensions: 213437
Number of successful extensions: 510
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 506
Number of HSP's gapped (non-prelim): 12
length of query: 182
length of database: 14,973,337
effective HSP length: 93
effective length of query: 89
effective length of database: 9,153,583
effective search space: 814668887
effective search space used: 814668887
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)