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= 022167
(301 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|Q Chain Q, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
Length = 332
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 31/107 (28%), Positives = 55/107 (51%), Gaps = 15/107 (14%)
Query: 205 LLTHAEVVRLSKKIKTGL----------SLDDHKLR--LKERLGCEPSMEQLAASLRISR 252
LLT E + L++K++ G+ LD +R ++ ++ +E++ L+
Sbjct: 17 LLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARVEEVDGKLKSLP 76
Query: 253 PELQSILM---ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
EL+ L E AR+ L+ +N+RLV+SIA++Y G DL+Q
Sbjct: 77 KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 123
>pdb|3UGO|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2
Complexed With -10 Promoter Element Ssdna Oligo (Tacaat)
pdb|3UGP|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2
Complexed With -10 Promoter Element Ssdna Oligo (Tataat)
pdb|4GOR|A Chain A, Crystallographic Analysis Of An Rna-Polymerase
Sigma-Subunit Fragment Complexed With -10 Promoter
Element Ssdna: G-Quadruplex Formation And Crystal
Packing
pdb|4GOR|B Chain B, Crystallographic Analysis Of An Rna-Polymerase
Sigma-Subunit Fragment Complexed With -10 Promoter
Element Ssdna: G-Quadruplex Formation And Crystal
Packing
Length = 245
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 37/144 (25%), Positives = 66/144 (45%), Gaps = 34/144 (23%)
Query: 185 SPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGL----------SLDDHKLR---- 230
P + + ++ Y+ + LLT E + L++K++ G+ LD +R
Sbjct: 1 GPHMTSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVR 60
Query: 231 --------------LKERLGCEP-SMEQLAASLRISRPELQ---SILMECSLAREKLVMS 272
LKE+ +P ++E++ L+ EL+ I E AR+ L+ +
Sbjct: 61 AKILGTARIQKIPGLKEK--PDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEA 118
Query: 273 NVRLVMSIAQRYDNMGADMADLVQ 296
N+RLV+SIA++Y G DL+Q
Sbjct: 119 NLRLVVSIAKKYTGRGLSFLDLIQ 142
>pdb|4G7H|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|P Chain P, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|P Chain P, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|P Chain P, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
Length = 443
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
I E AR+ L+ +N+RLV+SIA++Y G DL+Q
Sbjct: 196 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 234
>pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|P Chain P, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
Length = 423
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
I E AR+ L+ +N+RLV+SIA++Y G DL+Q
Sbjct: 176 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 214
>pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|P Chain P, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|F Chain F, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|P Chain P, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|F Chain F, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|P Chain P, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|2A68|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|P Chain P, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|3EQL|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
Length = 423
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
I E AR+ L+ +N+RLV+SIA++Y G DL+Q
Sbjct: 176 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 214
>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2
pdb|3LES|B Chain B, 2f5 Epitope Scaffold Es2
pdb|3LEV|A Chain A, Hiv-1 Antibody 2f5 In Complex With Epitope Scaffold Es2
Length = 179
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
I E AR+ L+ +N+RLV+SIA++Y G DL+Q
Sbjct: 99 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 137
>pdb|1KU2|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
Sigma Subunit Fragment Containing Regions 1.2 To 3.1
pdb|1KU2|B Chain B, Crystal Structure Of Thermus Aquaticus Rna Polymerase
Sigma Subunit Fragment Containing Regions 1.2 To 3.1
Length = 241
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
I E AR+ L+ +N+RLV+SIA++Y G DL+Q
Sbjct: 100 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 138
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
I E AR+ L+ +N+RLV+SIA++Y G DL+Q
Sbjct: 191 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 229
>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
Escherichia Coli Rna Polymerase
Length = 339
Score = 36.2 bits (82), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 25/32 (78%)
Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
A++++V +N+RLV+SIA++Y N G DL+Q
Sbjct: 266 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 297
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 613
Score = 35.8 bits (81), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 25/32 (78%)
Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
A++++V +N+RLV+SIA++Y N G DL+Q
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 406
>pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|Y Chain Y, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 613
Score = 35.8 bits (81), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 25/32 (78%)
Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
A++++V +N+RLV+SIA++Y N G DL+Q
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 406
>pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti-
Sigma Factor Spoiiab With The Sporulation Sigma Factor
Sigmaf
Length = 243
Score = 34.3 bits (77), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 23/33 (69%)
Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQV 297
AR++++ N+RLV S+ QR+ N G + DL Q+
Sbjct: 29 ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQI 61
>pdb|1RP3|A Chain A, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1RP3|C Chain C, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1RP3|E Chain E, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1RP3|G Chain G, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1SC5|A Chain A, Sigma-28(Flia)FLGM COMPLEX
Length = 239
Score = 31.2 bits (69), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 10/66 (15%)
Query: 230 RLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGA 289
+LKE+LG EP+ E++A L IS EL L + N ++S+ + + +
Sbjct: 107 KLKEKLGREPTDEEVAKELGISTEELFKTLDKI----------NFSYILSLEEVFRDFAR 156
Query: 290 DMADLV 295
D ++L+
Sbjct: 157 DYSELI 162
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
0.315 0.128 0.345
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,827,895
Number of Sequences: 62578
Number of extensions: 214609
Number of successful extensions: 539
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 521
Number of HSP's gapped (non-prelim): 20
length of query: 301
length of database: 14,973,337
effective HSP length: 98
effective length of query: 203
effective length of database: 8,840,693
effective search space: 1794660679
effective search space used: 1794660679
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)