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= 025558
(251 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2H9U|A Chain A, Crystal Structure Of The Archaea Specific Dna Binding
Protein
pdb|3U6Y|A Chain A, Crystal Structure Of Alba2-Dna Complex
pdb|3U6Y|C Chain C, Crystal Structure Of Alba2-Dna Complex
Length = 102
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 34/95 (35%), Positives = 48/95 (50%), Gaps = 5/95 (5%)
Query: 20 EIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRIAGLHQNTS 79
E+RI + M NY+ T L E+G+N++V+KA GR IN+ V E++++R A +N
Sbjct: 8 EVRIGRKPVM-NYVLAILTTLMEQGTNQVVVKARGRNINRAVDAVEIVRKRFA---KNIE 63
Query: 80 IGSTDITDMWXXXXXXXXXXXTTRHVSMITITLSK 114
I I D TR VS I I L K
Sbjct: 64 IKDIKI-DSQEIEVQTPEGQTRTRRVSSIEICLEK 97
>pdb|1H0X|A Chain A, Structure Of Alba: An Archaeal Chromatin Protein
Modulated By Acetylation
pdb|1H0X|B Chain B, Structure Of Alba: An Archaeal Chromatin Protein
Modulated By Acetylation
pdb|1H0Y|A Chain A, Structure Of Alba: An Archaeal Chromatin Protein
Modulated By Acetylation
Length = 100
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/63 (41%), Positives = 37/63 (58%), Gaps = 2/63 (3%)
Query: 8 EKPKAEAPINENEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELI 67
EK + P N + I + M NY+ A TLL + G +EIV+KA GRAI+K V E++
Sbjct: 2 EKMSSGTPTPSNVVLIGKKPVM-NYVLAALTLLNQ-GVSEIVIKARGRAISKAVDTVEIV 59
Query: 68 KRR 70
+ R
Sbjct: 60 RNR 62
>pdb|2BKY|A Chain A, Crystal Structure Of The Alba1:alba2 Heterodimer From
Sulfolobus Solfataricus
pdb|2BKY|B Chain B, Crystal Structure Of The Alba1:alba2 Heterodimer From
Sulfolobus Solfataricus
Length = 97
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/40 (50%), Positives = 28/40 (70%), Gaps = 1/40 (2%)
Query: 31 NYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRR 70
NY+ A TLL + G +EIV+KA GRAI+K V E+++ R
Sbjct: 21 NYVLAALTLLNQ-GVSEIVIKARGRAISKAVDTVEIVRNR 59
>pdb|1Y9X|A Chain A, Solution Structure Of Archaeon Dna-Binding Protein
Ssh10b
pdb|1Y9X|B Chain B, Solution Structure Of Archaeon Dna-Binding Protein
Ssh10b
Length = 97
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/40 (50%), Positives = 28/40 (70%), Gaps = 1/40 (2%)
Query: 31 NYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRR 70
NY+ A TLL + G +EIV+KA GRAI+K V E+++ R
Sbjct: 21 NYVLAALTLLNQ-GVSEIVIKARGRAISKAVDTVEIVRNR 59
>pdb|1NFH|A Chain A, Structure Of A Sir2 Substrate, Alba, Reveals A Mechanism
For Deactylation-Induced Enhancement Of Dna-Binding
pdb|1NFH|B Chain B, Structure Of A Sir2 Substrate, Alba, Reveals A Mechanism
For Deactylation-Induced Enhancement Of Dna-Binding
pdb|1NFJ|A Chain A, Structure Of A Sir2 Substrate, Alba, Reveals A Mechanism
For Deactylation-Induced Enhancement Of Dna-Binding
Length = 89
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 29/40 (72%), Gaps = 1/40 (2%)
Query: 31 NYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRR 70
NY+ T L E G++E+V+KA GRAI++ V +AE+++ R
Sbjct: 15 NYVLATLTQLNE-GADEVVIKARGRAISRAVDVAEIVRNR 53
>pdb|1NH9|A Chain A, Crystal Structure Of A Dna Binding Protein Mja10b From
The Hyperthermophile Methanococcus Jannaschii
Length = 87
Score = 35.4 bits (80), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 27/40 (67%), Gaps = 2/40 (5%)
Query: 31 NYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRR 70
NY+ L Q ++E+++KA G+AINK V +AE+I+ R
Sbjct: 14 NYVV--AVLTQLTSNDEVIIKARGKAINKAVDVAEMIRNR 51
>pdb|2Z7C|B Chain B, Crystal Structure Of Chromatin Protein Alba From
Hyperthermophilic Archaeon Pyrococcus Horikoshii
pdb|2Z7C|D Chain D, Crystal Structure Of Chromatin Protein Alba From
Hyperthermophilic Archaeon Pyrococcus Horikoshii
pdb|2Z7C|A Chain A, Crystal Structure Of Chromatin Protein Alba From
Hyperthermophilic Archaeon Pyrococcus Horikoshii
pdb|2Z7C|C Chain C, Crystal Structure Of Chromatin Protein Alba From
Hyperthermophilic Archaeon Pyrococcus Horikoshii
Length = 93
Score = 34.3 bits (77), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 26/40 (65%), Gaps = 1/40 (2%)
Query: 31 NYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRR 70
NY+ T E G+ E+ +KA GRAI++ V +AE+++ R
Sbjct: 16 NYVLAVITQFHE-GAKEVSIKARGRAISRAVDVAEIVRNR 54
>pdb|3TOE|A Chain A, Structure Of Mth10b
pdb|3TOE|B Chain B, Structure Of Mth10b
Length = 91
Score = 32.0 bits (71), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 27/40 (67%), Gaps = 1/40 (2%)
Query: 31 NYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRR 70
NY+ T + G++E++LKA G AI++ V +AE+++ R
Sbjct: 16 NYVLAVVTQMN-GGTSEVILKARGIAISRAVDVAEIVRNR 54
>pdb|2XCL|A Chain A, Nucleotide-Bound Structures Of Bacillus Subtilis
Glycinamide Ribonucleotide Synthetase
Length = 422
Score = 28.5 bits (62), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 36 ATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRIAGLH 75
A +QEKG+ IV+KA G A K V +A + IA LH
Sbjct: 129 AKAYVQEKGA-PIVIKADGLAAGKGVTVAXTEEEAIACLH 167
>pdb|2XD4|A Chain A, Nucleotide-Bound Structures Of Bacillus Subtilis
Glycinamide Ribonucleotide Synthetase
Length = 422
Score = 27.3 bits (59), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 36 ATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRIAGLH 75
A +QEKG+ IV+KA G A K V +A + IA LH
Sbjct: 129 AKAYVQEKGA-PIVIKADGLAAGKGVTVAMTEEEAIACLH 167
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
0.313 0.131 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,475,332
Number of Sequences: 62578
Number of extensions: 128966
Number of successful extensions: 115
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 105
Number of HSP's gapped (non-prelim): 14
length of query: 251
length of database: 14,973,337
effective HSP length: 96
effective length of query: 155
effective length of database: 8,965,849
effective search space: 1389706595
effective search space used: 1389706595
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)