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= psy5036
(176 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2LEF|A Chain A, Lef1 Hmg Domain (From Mouse), Complexed With Dna (15bp),
Nmr, 12 Structures
Length = 86
Score = 77.4 bits (189), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 36/56 (64%), Positives = 45/56 (80%), Gaps = 4/56 (7%)
Query: 80 TKPEARSGNEITNKNQMIQWHSLTREEQAKYYEKARQERQLHMELYPGWSARDNYG 135
T E+ + N+I + +WH+L+REEQAKYYE AR+ERQLHM+LYPGWSARDNYG
Sbjct: 26 TLKESAAINQILGR----RWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYG 77
>pdb|1DY6|A Chain A, Structure Of The Imipenem-Hydrolyzing Beta-Lactamase Sme-1
pdb|1DY6|B Chain B, Structure Of The Imipenem-Hydrolyzing Beta-Lactamase Sme-1
Length = 267
Score = 28.9 bits (63), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 22/44 (50%)
Query: 38 LLSDHNHSGMRWGGMSKPSIMSWHVGSVNFICNFILIGPQGQTK 81
+ + + SGM G M+ ++ G+ N I L GP+G TK
Sbjct: 84 ITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTK 127
>pdb|3NAA|H Chain H, Crystal Structure Of Fab15 Mut5
pdb|3NCJ|H Chain H, Crystal Structure Of Fab15 Mut8
Length = 225
Score = 28.5 bits (62), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 34/83 (40%), Gaps = 15/83 (18%)
Query: 46 GMRWGGMSKPSIMSWHVGSVNFICNFILIGPQGQTKPEARSGNEITNKNQMIQWHSLTRE 105
G+ W G PS N+ +F QGQ A + + +QW SL
Sbjct: 44 GLEWMGFIDPSD-----SYTNYAPSF-----QGQVTISA----DKSISTAYLQWSSLKAS 89
Query: 106 EQAKYYEKARQERQLHMELYPGW 128
+ A YY ARQ Q +M+ + W
Sbjct: 90 DTAMYY-CARQLYQGYMDTFDSW 111
>pdb|3NAC|H Chain H, Crystal Structure Of Fab15 Mut7
Length = 225
Score = 28.1 bits (61), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 97 IQWHSLTREEQAKYYEKARQERQLHMELYPGW 128
+QW SL + A YY ARQ Q +M+ + W
Sbjct: 81 LQWSSLKASDTAMYY-CARQLYQGYMDTFDSW 111
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 27.7 bits (60), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 25/47 (53%)
Query: 85 RSGNEITNKNQMIQWHSLTREEQAKYYEKARQERQLHMELYPGWSAR 131
R N +K QW LT E+ ++++A++ + +H E YP + R
Sbjct: 29 RMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR 75
>pdb|1O4X|B Chain B, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 88
Score = 27.3 bits (59), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 65 VNFICNFILIGPQGQTKPEARSGNEITN----KNQMIQWHSLTREEQAKYYEKARQERQL 120
V N ++ +GQ + A+ ++ N K +W L+ E+ + ++A++ R L
Sbjct: 8 VKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRAL 67
Query: 121 HMELYPGWSAR 131
HM+ +P + R
Sbjct: 68 HMKEHPDYKYR 78
>pdb|1BUE|A Chain A, Nmc-A Carbapenemase From Enterobacter Cloacae
pdb|1BUL|A Chain A, 6alpha-(Hydroxypropyl)penicillanate Acylated On Nmc-A
Beta- Lactamase From Enterobacter Cloacae
Length = 265
Score = 26.9 bits (58), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 25/52 (48%)
Query: 38 LLSDHNHSGMRWGGMSKPSIMSWHVGSVNFICNFILIGPQGQTKPEARSGNE 89
+ + + +GM G M+ ++ G+ N I + GP+G TK G+E
Sbjct: 82 ITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDE 133
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 26.6 bits (57), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 65 VNFICNFILIGPQGQTKPEARSGNEITN----KNQMIQWHSLTREEQAKYYEKARQERQL 120
V N ++ +GQ + A+ ++ N K +W L+ E+ + ++A++ R L
Sbjct: 4 VKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRAL 63
Query: 121 HMELYPGWSAR 131
HM+ +P + R
Sbjct: 64 HMKEHPDYKYR 74
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 26.2 bits (56), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 65 VNFICNFILIGPQGQTKPEARSGNEITN----KNQMIQWHSLTREEQAKYYEKARQERQL 120
V N ++ +GQ + A+ ++ N K +W L+ E+ + ++A++ R L
Sbjct: 3 VKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRAL 62
Query: 121 HMELYPGWSAR 131
HM+ +P + R
Sbjct: 63 HMKEHPDYKYR 73
>pdb|1HRZ|A Chain A, The 3d Structure Of The Human Sry-Dna Complex Solved By
Multi-Dimensional Heteronuclear-Edited And-Filtered Nmr
pdb|1HRY|A Chain A, The 3d Structure Of The Human Sry-Dna Complex Solved By
Multid-Dimensional Heteronuclear-Edited And-Filtered Nmr
Length = 76
Score = 26.2 bits (56), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 25/47 (53%)
Query: 85 RSGNEITNKNQMIQWHSLTREEQAKYYEKARQERQLHMELYPGWSAR 131
R N +K QW LT E+ ++++A++ + +H E YP + R
Sbjct: 29 RMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR 75
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
0.317 0.132 0.415
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,696,104
Number of Sequences: 62578
Number of extensions: 223980
Number of successful extensions: 448
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 435
Number of HSP's gapped (non-prelim): 16
length of query: 176
length of database: 14,973,337
effective HSP length: 92
effective length of query: 84
effective length of database: 9,216,161
effective search space: 774157524
effective search space used: 774157524
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)