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= 006305
(651 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3S1S|A Chain A, Characterization And Crystal Structure Of The Type Iig
Restriction Endonuclease Bpusi
Length = 878
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 28/95 (29%), Positives = 46/95 (48%), Gaps = 15/95 (15%)
Query: 266 PNTENKSFTPSSIYVGSFTDSQSDNGERLL----------GNETDNCKISDS---EVNEC 312
P + PS I VG+F+D+ S+ RL+ N+ K S + ++ E
Sbjct: 127 PVVSQQIIEPSPIVVGNFSDTVSEFYNRLVEAFQNIIDISVNDAGTYKSSTANLVDILEN 186
Query: 313 EPNSSTSWASALAIEPDKNVKAV--GRNVMVPSVD 345
++STSW AL + + ++ V G+NV VP+ D
Sbjct: 187 RKDNSTSWHQALVVAGYEYIRGVLRGQNVEVPTRD 221
>pdb|1TTU|A Chain A, Crystal Structure Of Csl Bound To Dna
pdb|2FO1|A Chain A, Crystal Structure Of The Csl-Notch-Mastermind Ternary
Complex Bound To Dna
pdb|3BRD|A Chain A, Csl (Lag-1) Bound To Dna With Lin-12 Ram Peptide, P212121
Length = 477
Score = 33.9 bits (76), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 43/88 (48%), Gaps = 19/88 (21%)
Query: 59 NDSVKTLTEKLSAALLNVSAKEDLVKQ--HAKVAEEAVS-----------------GWEK 99
DSV++LT L+ K + V HAKVA+++ GW+
Sbjct: 6 GDSVQSLTSDRMIDFLSNKEKYECVISIFHAKVAQKSYGNEKRFFCPPPCIYLIGQGWKL 65
Query: 100 AENELSTLKQQLKAASQKNSALENRVSH 127
++ ++ L + LKA++QK++A+EN H
Sbjct: 66 KKDRVAQLYKTLKASAQKDAAIENDPIH 93
>pdb|3BRF|A Chain A, Csl (Lag-1) Bound To Dna With Lin-12 Ram Peptide, C2221
Length = 478
Score = 33.9 bits (76), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 43/88 (48%), Gaps = 19/88 (21%)
Query: 59 NDSVKTLTEKLSAALLNVSAKEDLVKQ--HAKVAEEAVS-----------------GWEK 99
DSV++LT L+ K + V HAKVA+++ GW+
Sbjct: 7 GDSVQSLTSDRMIDFLSNKEKYECVISIFHAKVAQKSYGNEKRFFCPPPCIYLIGQGWKL 66
Query: 100 AENELSTLKQQLKAASQKNSALENRVSH 127
++ ++ L + LKA++QK++A+EN H
Sbjct: 67 KKDRVAQLYKTLKASAQKDAAIENDPIH 94
>pdb|1QVR|A Chain A, Crystal Structure Analysis Of Clpb
pdb|1QVR|B Chain B, Crystal Structure Analysis Of Clpb
pdb|1QVR|C Chain C, Crystal Structure Analysis Of Clpb
Length = 854
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 33/53 (62%), Gaps = 4/53 (7%)
Query: 513 RLRAVEAEMETLRSKVISLEDEVEKERALSEENIANFQKSKDELSKVKQEIEL 565
RL+A+EAE+ L ++ L E E+ER E + ++++ L +V++EIEL
Sbjct: 431 RLKAIEAEIAKLTEEIAKLRAEWERER----EILRKLREAQHRLDEVRREIEL 479
>pdb|3E6A|O Chain O, Crystal Structure And Functional Analysis Of
Glyceraldehyde- 3-Phosphate Dehydrogenase From Oryza
Sativa
pdb|3E6A|A Chain A, Crystal Structure And Functional Analysis Of
Glyceraldehyde- 3-Phosphate Dehydrogenase From Oryza
Sativa
pdb|3E6A|B Chain B, Crystal Structure And Functional Analysis Of
Glyceraldehyde- 3-Phosphate Dehydrogenase From Oryza
Sativa
pdb|3E6A|C Chain C, Crystal Structure And Functional Analysis Of
Glyceraldehyde- 3-Phosphate Dehydrogenase From Oryza
Sativa
Length = 336
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 316 SSTSWASALA-IEPDKNVKAVGRNVMVPSVDINLMDDFLEMERLAAL 361
SST A A+ + PD N K G + VP+VD++++D + +E+ A+
Sbjct: 210 SSTGAAKAVGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASY 256
>pdb|3E5R|O Chain O, Crystal Structure And Functional Analysis Of
Glyceraldehyde- 3-Phosphate Dehydrogenase From Oryza
Sativa
pdb|3E5R|A Chain A, Crystal Structure And Functional Analysis Of
Glyceraldehyde- 3-Phosphate Dehydrogenase From Oryza
Sativa
pdb|3E5R|B Chain B, Crystal Structure And Functional Analysis Of
Glyceraldehyde- 3-Phosphate Dehydrogenase From Oryza
Sativa
pdb|3E5R|C Chain C, Crystal Structure And Functional Analysis Of
Glyceraldehyde- 3-Phosphate Dehydrogenase From Oryza
Sativa
pdb|3V1Y|O Chain O, Crystal Structures Of Glyceraldehyde-3-Phosphate
Dehydrogenase Complexes With Nad
pdb|3V1Y|A Chain A, Crystal Structures Of Glyceraldehyde-3-Phosphate
Dehydrogenase Complexes With Nad
pdb|3V1Y|B Chain B, Crystal Structures Of Glyceraldehyde-3-Phosphate
Dehydrogenase Complexes With Nad
pdb|3V1Y|C Chain C, Crystal Structures Of Glyceraldehyde-3-Phosphate
Dehydrogenase Complexes With Nad
Length = 337
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 316 SSTSWASALA-IEPDKNVKAVGRNVMVPSVDINLMDDFLEMERLAAL 361
SST A A+ + PD N K G + VP+VD++++D + +E+ A+
Sbjct: 211 SSTGAAKAVGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASY 257
>pdb|4HSE|A Chain A, Crystal Structure Of Clpb Nbd1 In Complex With Guanidinium
Chloride And Adp
Length = 397
Score = 29.6 bits (65), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 33/53 (62%), Gaps = 4/53 (7%)
Query: 513 RLRAVEAEMETLRSKVISLEDEVEKERALSEENIANFQKSKDELSKVKQEIEL 565
RL+A+EAE+ L ++ L E E+ER E + ++++ L +V++EIEL
Sbjct: 294 RLKAIEAEIAKLTEEIAKLRAEWERER----EILRKLREAQHRLDEVRREIEL 342
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
0.306 0.120 0.314
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,767,903
Number of Sequences: 62578
Number of extensions: 409442
Number of successful extensions: 1175
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1154
Number of HSP's gapped (non-prelim): 34
length of query: 651
length of database: 14,973,337
effective HSP length: 105
effective length of query: 546
effective length of database: 8,402,647
effective search space: 4587845262
effective search space used: 4587845262
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 55 (25.8 bits)