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= 042002
(143 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 = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 31/95 (32%), Positives = 46/95 (48%), Gaps = 5/95 (5%)
Query: 20 EIRITTQGRMRNYITYATTLLQEKGSNEISLKAMGRAINKTVMIAELIKRRIVGLHQNTA 79
E+RI + M NY+ T L E+G+N++ +KA GR IN+ V E++++R +N
Sbjct: 8 EVRIGRKPVM-NYVLAILTTLMEQGTNQVVVKARGRNINRAVDAVEIVRKR---FAKNIE 63
Query: 80 IGSTDITDMWXXXXXXXXXXXTTRHVSVITVTLSK 114
I I D TR VS 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 = 39.3 bits (90), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 39/66 (59%), Gaps = 2/66 (3%)
Query: 7 VEKPKAETPINENEIRITTQGRMRNYITYATTLLQEKGSNEISLKAMGRAINKTVMIAEL 66
+EK + TP N + I + M NY+ A TLL + G +EI +KA GRAI+K V E+
Sbjct: 1 MEKMSSGTPTPSNVVLIGKKPVM-NYVLAALTLLNQ-GVSEIVIKARGRAISKAVDTVEI 58
Query: 67 IKRRIV 72
++ R +
Sbjct: 59 VRNRFL 64
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 31 NYITYATTLLQEKGSNEISLKAMGRAINKTVMIAELIKRRIV 72
NY+ T E G+ E+S+KA GRAI++ V +AE+++ R +
Sbjct: 16 NYVLAVITQFHE-GAKEVSIKARGRAISRAVDVAEIVRNRFL 56
>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 = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 14 TPINENEIRITTQGRMRNYITYATTLLQEKGSNEISLKAMGRAINKTVMIAELIKRRIV 72
TP N + I + M NY+ A TLL + G +EI +KA GRAI+K V E+++ R +
Sbjct: 5 TPTPSNVVLIGKKPVM-NYVLAALTLLNQ-GVSEIVIKARGRAISKAVDTVEIVRNRFL 61
>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 = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 14 TPINENEIRITTQGRMRNYITYATTLLQEKGSNEISLKAMGRAINKTVMIAELIKRRIVG 73
TP N + I + M NY+ A TLL + G +EI +KA GRAI+K V E+++ R +
Sbjct: 5 TPTPSNVVLIGKKPVM-NYVLAALTLLNQ-GVSEIVIKARGRAISKAVDTVEIVRNRFLA 62
>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 = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 1/41 (2%)
Query: 31 NYITYATTLLQEKGSNEISLKAMGRAINKTVMIAELIKRRI 71
NY+ T L E G++E+ +KA GRAI++ V +AE+++ R
Sbjct: 15 NYVLATLTQLNE-GADEVVIKARGRAISRAVDVAEIVRNRF 54
>pdb|1NH9|A Chain A, Crystal Structure Of A Dna Binding Protein Mja10b From
The Hyperthermophile Methanococcus Jannaschii
Length = 87
Score = 33.9 bits (76), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 26/41 (63%), Gaps = 2/41 (4%)
Query: 31 NYITYATTLLQEKGSNEISLKAMGRAINKTVMIAELIKRRI 71
NY+ L Q ++E+ +KA G+AINK V +AE+I+ R
Sbjct: 14 NYVV--AVLTQLTSNDEVIIKARGKAINKAVDVAEMIRNRF 52
>pdb|3TOE|A Chain A, Structure Of Mth10b
pdb|3TOE|B Chain B, Structure Of Mth10b
Length = 91
Score = 30.8 bits (68), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 27/42 (64%), Gaps = 1/42 (2%)
Query: 31 NYITYATTLLQEKGSNEISLKAMGRAINKTVMIAELIKRRIV 72
NY+ T + G++E+ LKA G AI++ V +AE+++ R +
Sbjct: 16 NYVLAVVTQMN-GGTSEVILKARGIAISRAVDVAEIVRNRFI 56
>pdb|2QKX|A Chain A, N-Acetyl Glucosamine 1-Phosphate Uridyltransferase From
Mycobacterium Tuberculosis Complex With N-Acetyl
Glucosamine 1-Phosphate
Length = 391
Score = 27.3 bits (59), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 7/65 (10%)
Query: 32 YITYATTLLQEKG----SNEISLKAMGRAINKTVMIAEL---IKRRIVGLHQNTAIGSTD 84
Y+T +L+ G ++ + A+ +N V +AEL + RR+V HQ + D
Sbjct: 211 YLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVD 270
Query: 85 ITDMW 89
W
Sbjct: 271 PATTW 275
>pdb|3SPT|A Chain A, Crystal Structure Of Glmu From Mycobacterium Tuberculosis
In Complex With Acetyl Coenzyme A And
Uridine-Diphosphate-N-Acetylglucosamine
pdb|3ST8|A Chain A, Crystal Structure Of Glmu From Mycobacterium Tuberculosis
In Complex With Coenzyme A, Glucosamine 1-Phosphate And
Uridine-Diphosphate-N- Acetylglucosamine
Length = 501
Score = 26.6 bits (57), Expect = 4.9, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 7/65 (10%)
Query: 32 YITYATTLLQEKG----SNEISLKAMGRAINKTVMIAEL---IKRRIVGLHQNTAIGSTD 84
Y+T +L+ G ++ + A+ +N V +AEL + RR+V HQ + D
Sbjct: 215 YLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVD 274
Query: 85 ITDMW 89
W
Sbjct: 275 PATTW 279
>pdb|3D8V|A Chain A, Crystal Structure Of Glmu From Mycobacterium Tuberculosis
In Complex With Uridine-Diphosphate-N-Acetylglucosamine
pdb|3D98|A Chain A, Crystal Structure Of Glmu From Mycobacterium Tuberculosis,
Ligand-Free Form
pdb|3DJ4|A Chain A, Crystal Structure Of Glmu From Mycobacterium Tuberculosis
In Complex With Uridine-Diphosphate-N-Acetylglucosamine.
pdb|3DK5|A Chain A, Crystal Structure Of Apo-Glmu From Mycobacterium
Tuberculosis
Length = 495
Score = 26.6 bits (57), Expect = 4.9, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 7/65 (10%)
Query: 32 YITYATTLLQEKG----SNEISLKAMGRAINKTVMIAEL---IKRRIVGLHQNTAIGSTD 84
Y+T +L+ G ++ + A+ +N V +AEL + RR+V HQ + D
Sbjct: 209 YLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVD 268
Query: 85 ITDMW 89
W
Sbjct: 269 PATTW 273
>pdb|3FOQ|A Chain A, Crystal Structure Of N-Acetylglucosamine-1-Phosphate
Uridyltransferase (Glmu) From Mycobacterium Tuberculosis
In A Cubic Space Group
Length = 503
Score = 26.6 bits (57), Expect = 5.0, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 7/65 (10%)
Query: 32 YITYATTLLQEKG----SNEISLKAMGRAINKTVMIAEL---IKRRIVGLHQNTAIGSTD 84
Y+T +L+ G ++ + A+ +N V +AEL + RR+V HQ + D
Sbjct: 217 YLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVD 276
Query: 85 ITDMW 89
W
Sbjct: 277 PATTW 281
>pdb|1VM0|A Chain A, X-Ray Structure Of Gene Product From Arabidopsis
Thaliana At2g34160
pdb|1VM0|B Chain B, X-Ray Structure Of Gene Product From Arabidopsis
Thaliana At2g34160
pdb|2Q3V|A Chain A, Ensemble Refinement Of The Protein Crystal Structure Of
Gene Product From Arabidopsis Thaliana At2g34160
pdb|2Q3V|B Chain B, Ensemble Refinement Of The Protein Crystal Structure Of
Gene Product From Arabidopsis Thaliana At2g34160
Length = 130
Score = 25.8 bits (55), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 20/42 (47%)
Query: 46 NEISLKAMGRAINKTVMIAELIKRRIVGLHQNTAIGSTDITD 87
N++ L A+G AI V + E++K + + DI D
Sbjct: 47 NDVELSALGXAIATVVTVTEILKNNGFAVEKKIXTSIVDIKD 88
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
0.314 0.129 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,536,245
Number of Sequences: 62578
Number of extensions: 102521
Number of successful extensions: 126
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 112
Number of HSP's gapped (non-prelim): 20
length of query: 143
length of database: 14,973,337
effective HSP length: 89
effective length of query: 54
effective length of database: 9,403,895
effective search space: 507810330
effective search space used: 507810330
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 46 (22.3 bits)