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= 039421
(112 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3AL0|C Chain C, Crystal Structure Of The Glutamine Transamidosome From
Thermotoga Maritima In The Glutamylation State
Length = 592
Score = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 1 MGIKM-QDMVLHAKQIIRRRLSSNNKQQQFSSYQ 33
MGIK+ +D+VLH + + R LS + ++ +Q
Sbjct: 1 MGIKVTKDLVLHLENLARLELSEDQRESLMKDFQ 34
>pdb|3C2W|A Chain A, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|B Chain B, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|C Chain C, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|D Chain D, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|E Chain E, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|F Chain F, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|G Chain G, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|H Chain H, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3NHQ|A Chain A, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|B Chain B, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|C Chain C, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|D Chain D, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|E Chain E, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|F Chain F, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|G Chain G, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|H Chain H, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NOP|C Chain C, Light-Induced Intermediate Structure L1 Of Pseudomonas
Aeruginosa Bacteriophytochrome
pdb|3NOT|C Chain C, Light-Induced Intermediate Structure L2 Of P. Aeruginosa
Bacteriophytochrome
pdb|3NOU|C Chain C, Light-Induced Intermediate Structure L3 Of P. Aeruginosa
Bacteriophytochrome
Length = 505
Score = 26.9 bits (58), Expect = 2.7, Method: Composition-based stats.
Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 6/67 (8%)
Query: 22 SNNKQQQFSSY--QTSTASDVPKGHFAIYVGQEDKKKKRFVVPISYLKHPLFQALLSQAE 79
+ ++++ SY Q ASD+P +Y+ + R + ++Y +F AL +
Sbjct: 175 AESRREDLESYLGQRYPASDIPAQARRLYI----QNPIRLIADVAYTPMRVFPALNPETN 230
Query: 80 EEFGFDY 86
E F Y
Sbjct: 231 ESFDLSY 237
>pdb|2PMZ|B Chain B, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|R Chain R, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|B Chain B, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|J Chain J, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 1124
Score = 26.2 bits (56), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 48 YVGQEDKKKKRFVVPISYLKHPLFQALLSQA 78
Y+G DK K ++V PI K LF +S A
Sbjct: 1066 YIGWYDKNKNKYVCPIHGDKSNLFPVTVSYA 1096
>pdb|2WAQ|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|R Chain R, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|B Chain B, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|R Chain R, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|B Chain B, Rnap At 3.2ang
pdb|4B1O|B Chain B, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|R Chain R, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 1131
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 48 YVGQEDKKKKRFVVPISYLKHPLFQALLSQA 78
Y+G DK K ++V PI K LF +S A
Sbjct: 1069 YIGWYDKNKNKYVCPIHGDKSNLFPVTVSYA 1099
>pdb|1H99|A Chain A, Prd Of Lict Antiterminator From Bacillus Subtilis
Length = 224
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 21/46 (45%)
Query: 40 VPKGHFAIYVGQEDKKKKRFVVPISYLKHPLFQALLSQAEEEFGFD 85
+ K HF I +E RFV + + LF ++E++F D
Sbjct: 132 IVKYHFKIEFNEESLHYYRFVTDLKFFAQRLFNGTHMESEDDFLLD 177
>pdb|3LUZ|A Chain A, Crystal Structure Of Extragenic Suppressor Protein Suhb
From Bartonella Henselae, Via Combined Iodide Sad
Molecular Replacement
pdb|3LUZ|B Chain B, Crystal Structure Of Extragenic Suppressor Protein Suhb
From Bartonella Henselae, Via Combined Iodide Sad
Molecular Replacement
pdb|3LV0|A Chain A, Crystal Structure Of Extragenic Suppressor Protein Suhb
From Bartonella Henselae, Native
pdb|3LV0|B Chain B, Crystal Structure Of Extragenic Suppressor Protein Suhb
From Bartonella Henselae, Native
Length = 267
Score = 25.0 bits (53), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 46 AIYVGQEDKKKKRFVVPISYLKHPLFQALLSQAEEEFGFDYRMHGITIPC-GEDEFL 101
A YV Q D+K ++ + P F L+ ++EE G D + I P G FL
Sbjct: 43 ADYVSQADRKAEKIIFNELSKARPKFGFLMEESEEIIGEDSQHRFIVDPLDGTTNFL 99
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
0.321 0.135 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,085,983
Number of Sequences: 62578
Number of extensions: 112332
Number of successful extensions: 313
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 305
Number of HSP's gapped (non-prelim): 10
length of query: 112
length of database: 14,973,337
effective HSP length: 76
effective length of query: 36
effective length of database: 10,217,409
effective search space: 367826724
effective search space used: 367826724
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)