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= 028304
(210 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 = 47.0 bits (110), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 33/95 (34%), Positives = 49/95 (51%), Gaps = 5/95 (5%)
Query: 20 EIRITSQGRMRSYITYAMTLLQERGSNEIVFKAMGRAINKTVTIVELIKRRIVGLHQNTV 79
E+RI + M +Y+ +T L E+G+N++V KA GR IN+ V VE++++R +N
Sbjct: 8 EVRIGRKPVM-NYVLAILTTLMEQGTNQVVVKARGRNINRAVDAVEIVRKR---FAKNIE 63
Query: 80 IGSTDITDTWXXXXXXXXXXXTTRHVSMITITLSK 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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/63 (42%), Positives = 39/63 (61%), Gaps = 2/63 (3%)
Query: 8 EKPKAETPIDENEIRITSQGRMRSYITYAMTLLQERGSNEIVFKAMGRAINKTVTIVELI 67
EK + TP N + I + M +Y+ A+TLL + G +EIV KA GRAI+K V VE++
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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 36/57 (63%), Gaps = 2/57 (3%)
Query: 14 TPIDENEIRITSQGRMRSYITYAMTLLQERGSNEIVFKAMGRAINKTVTIVELIKRR 70
TP N + I + M +Y+ A+TLL + G +EIV KA GRAI+K V VE+++ R
Sbjct: 5 TPTPSNVVLIGKKPVM-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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 36/57 (63%), Gaps = 2/57 (3%)
Query: 14 TPIDENEIRITSQGRMRSYITYAMTLLQERGSNEIVFKAMGRAINKTVTIVELIKRR 70
TP N + I + M +Y+ A+TLL + G +EIV KA GRAI+K V VE+++ R
Sbjct: 5 TPTPSNVVLIGKKPVM-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 = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 28/40 (70%), Gaps = 1/40 (2%)
Query: 31 SYITYAMTLLQERGSNEIVFKAMGRAINKTVTIVELIKRR 70
+Y+ +T L E G++E+V KA GRAI++ V + E+++ 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 = 35.0 bits (79), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 27/42 (64%), Gaps = 1/42 (2%)
Query: 30 RSYITYAMTLLQERGSN-EIVFKAMGRAINKTVTIVELIKRR 70
+ + Y + +L + SN E++ KA G+AINK V + E+I+ R
Sbjct: 10 KPVMNYVVAVLTQLTSNDEVIIKARGKAINKAVDVAEMIRNR 51
>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 = 26.9 bits (58), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 7/65 (10%)
Query: 32 YITYAMTLLQERG----SNEIVFKAMGRAINKTVTIVEL---IKRRIVGLHQNTVIGSTD 84
Y+T + +L+ G ++ + A+ +N V + EL + RR+V HQ + D
Sbjct: 217 YLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVD 276
Query: 85 ITDTW 89
TW
Sbjct: 277 PATTW 281
>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 = 9.3, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 7/65 (10%)
Query: 32 YITYAMTLLQERG----SNEIVFKAMGRAINKTVTIVEL---IKRRIVGLHQNTVIGSTD 84
Y+T + +L+ G ++ + A+ +N V + EL + RR+V HQ + D
Sbjct: 215 YLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVD 274
Query: 85 ITDTW 89
TW
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 = 9.3, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 7/65 (10%)
Query: 32 YITYAMTLLQERG----SNEIVFKAMGRAINKTVTIVEL---IKRRIVGLHQNTVIGSTD 84
Y+T + +L+ G ++ + A+ +N V + EL + RR+V HQ + D
Sbjct: 209 YLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVD 268
Query: 85 ITDTW 89
TW
Sbjct: 269 PATTW 273
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
0.324 0.137 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,954,402
Number of Sequences: 62578
Number of extensions: 149950
Number of successful extensions: 355
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 348
Number of HSP's gapped (non-prelim): 12
length of query: 210
length of database: 14,973,337
effective HSP length: 95
effective length of query: 115
effective length of database: 9,028,427
effective search space: 1038269105
effective search space used: 1038269105
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 49 (23.5 bits)