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= 028219
(212 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1MQS|A Chain A, Crystal Structure Of Sly1p In Complex With An N-Terminal
Peptide Of Sed5p
Length = 671
Score = 31.2 bits (69), Expect = 0.48, Method: Composition-based stats.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 4/88 (4%)
Query: 35 NKAADEIGKLNPLTQMPEKTGGGNSGMRFHVALTATDAIYSQWQSRIMYYWYKKVKDMPR 94
N D + + ++PE T N+ + H + A A+ SQ +S+ + +++ +D
Sbjct: 377 NSNNDTVQIQEVVKKLPELTAKKNT-IDTHXNIFA--ALLSQLESKSLDTFFEVEQDPGS 433
Query: 95 SDM-GKFTRILHSGKADNLMDEIPSFVV 121
+ +F IL GK +NL D++ SF+V
Sbjct: 434 TKTRSRFLDILKDGKTNNLEDKLRSFIV 461
>pdb|1CYX|A Chain A, Quinol Oxidase (Periplasmic Fragment Of Subunit Ii With
Engineered Cu-A Binding Site)(Cyoa)
Length = 205
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 10/54 (18%)
Query: 52 EKTGGGNSGMRFHVALTATDAIYSQWQSRIMYYWYKKVKDMPR--SDMGKFTRI 103
E G G+SGM+F T A + QW + K K P SDM F ++
Sbjct: 99 EICGPGHSGMKFKAIATPDRAAFDQWVA--------KAKQSPNTMSDMAAFEKL 144
>pdb|1TUF|A Chain A, Crystal Structure Of Diaminopimelate Decarboxylase From M.
Jannaschi
pdb|1TUF|B Chain B, Crystal Structure Of Diaminopimelate Decarboxylase From M.
Jannaschi
Length = 434
Score = 28.5 bits (62), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 189 WDPEVGKRFILHYTYGCDYNLKV 211
W+ E GK FI+ Y Y + NL +
Sbjct: 54 WEEETGKEFIVAYAYXANANLAI 76
>pdb|1TWI|A Chain A, Crystal Structure Of Diaminopimelate Decarboxylase From M.
Jannaschii In Co-Complex With L-Lysine
pdb|1TWI|B Chain B, Crystal Structure Of Diaminopimelate Decarboxylase From M.
Jannaschii In Co-Complex With L-Lysine
pdb|1TWI|C Chain C, Crystal Structure Of Diaminopimelate Decarboxylase From M.
Jannaschii In Co-Complex With L-Lysine
pdb|1TWI|D Chain D, Crystal Structure Of Diaminopimelate Decarboxylase From M.
Jannaschii In Co-Complex With L-Lysine
Length = 434
Score = 28.5 bits (62), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 189 WDPEVGKRFILHYTYGCDYNLKV 211
W+ E GK FI+ Y Y + NL +
Sbjct: 54 WEEETGKEFIVAYAYKANANLAI 76
>pdb|3B33|A Chain A, Crystal Structure Of The Pas Domain Of Nitrogen Regulation
Protein Nr(Ii) From Vibrio Parahaemolyticus
Length = 115
Score = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 7/84 (8%)
Query: 58 NSGMRFHVALTATDAIYSQWQSRIMYYWYKKVKDMPRSDMGKFTRILHSGKADNLMDEIP 117
+ G+ A A + ++SQ RI+ ++ D+ T+ L SG++ + D
Sbjct: 24 DDGLAIRYANPAAELLFSQSAKRIVEQSLSQLIQHASLDLALLTQPLQSGQS--ITDSDV 81
Query: 118 SFVVDPLPEGLDRYLLEEISP-TW 140
+FVVD P L+ +SP TW
Sbjct: 82 TFVVDGRPLXLEVT----VSPITW 101
>pdb|4GZY|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
pdb|4GZZ|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
Length = 1534
Score = 28.1 bits (61), Expect = 3.3, Method: Composition-based stats.
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 125 PEGLDRYLLEEISPTWLNVSLRMKDDH 151
PE ++RYL+EEI + +++ D H
Sbjct: 1341 PEAVERYLVEEIQKVYRAQGVKLHDKH 1367
>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|N Chain N, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|D Chain D, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|N Chain N, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|D Chain D, Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme
In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|N Chain N, Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme
In Complex With The Antibiotic Streptolydigin
pdb|2A68|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2O5I|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5I|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5J|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2O5J|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2PPB|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|2PPB|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|3DXJ|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3EQL|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3AOH|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOI|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|4G7H|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
Length = 1524
Score = 28.1 bits (61), Expect = 3.3, Method: Composition-based stats.
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 125 PEGLDRYLLEEISPTWLNVSLRMKDDH 151
PE ++RYL+EEI + +++ D H
Sbjct: 1341 PEAVERYLVEEIQKVYRAQGVKLHDKH 1367
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 0.137 0.430
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,268,403
Number of Sequences: 62578
Number of extensions: 256309
Number of successful extensions: 524
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 520
Number of HSP's gapped (non-prelim): 8
length of query: 212
length of database: 14,973,337
effective HSP length: 95
effective length of query: 117
effective length of database: 9,028,427
effective search space: 1056325959
effective search space used: 1056325959
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)