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= 017044
(378 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 = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 43/125 (34%), Positives = 67/125 (53%), Gaps = 21/125 (16%)
Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 310
+DP+R +L LLT +EE +L ++++ I+ E + L + RE + AK
Sbjct: 2 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 58
Query: 311 AIGLS------------CRDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISL 355
+G + ++LK LH G ++R+ LI ANLRLVV +AK+Y GRG+S
Sbjct: 59 ILGTARVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSF 118
Query: 356 HDLLQ 360
DL+Q
Sbjct: 119 LDLIQ 123
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 43/140 (30%), Positives = 67/140 (47%), Gaps = 36/140 (25%)
Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 310
+DP+R +L LLT +EE +L ++++ I+ E + L + RE + AK
Sbjct: 93 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 149
Query: 311 AIGLS---------------------------CRDLKSELH---SGNSSREKLINANLRL 340
+G + ++LK LH G ++R+ LI ANLRL
Sbjct: 150 ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 209
Query: 341 VVHVAKQYQGRGISLHDLLQ 360
VV +AK+Y GRG+S DL+Q
Sbjct: 210 VVSIAKKYTGRGLSFLDLIQ 229
>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 = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 25/47 (53%), Positives = 34/47 (72%), Gaps = 3/47 (6%)
Query: 317 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
++LK LH G ++R+ LI ANLRLVV +AK+Y GRG+S DL+Q
Sbjct: 92 KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 138
>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 = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 43/140 (30%), Positives = 67/140 (47%), Gaps = 36/140 (25%)
Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 310
+DP+R +L LLT +EE +L ++++ I+ E + L + RE + AK
Sbjct: 6 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 62
Query: 311 AIGLS---------------------------CRDLKSELH---SGNSSREKLINANLRL 340
+G + ++LK LH G ++R+ LI ANLRL
Sbjct: 63 ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 122
Query: 341 VVHVAKQYQGRGISLHDLLQ 360
VV +AK+Y GRG+S DL+Q
Sbjct: 123 VVSIAKKYTGRGLSFLDLIQ 142
>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 = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/47 (53%), Positives = 34/47 (72%), Gaps = 3/47 (6%)
Query: 317 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
++LK LH G ++R+ LI ANLRLVV +AK+Y GRG+S DL+Q
Sbjct: 91 KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 137
>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 = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 21/35 (60%), Positives = 28/35 (80%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
G ++R+ LI ANLRLVV +AK+Y GRG+S DL+Q
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 214
Score = 28.1 bits (61), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 22/35 (62%)
Query: 279 IAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIG 313
+ ++ + +L + +LQ + GREPT E A+A+G
Sbjct: 262 VHMVETINKLSRTARQLQQELGREPTYEEIAEAMG 296
>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 = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 21/35 (60%), Positives = 28/35 (80%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
G ++R+ LI ANLRLVV +AK+Y GRG+S DL+Q
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 214
Score = 28.1 bits (61), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 22/35 (62%)
Query: 279 IAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIG 313
+ ++ + +L + +LQ + GREPT E A+A+G
Sbjct: 262 VHMVETINKLSRTARQLQQELGREPTYEEIAEAMG 296
>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 = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 21/35 (60%), Positives = 28/35 (80%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
G ++R+ LI ANLRLVV +AK+Y GRG+S DL+Q
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 234
Score = 28.1 bits (61), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 22/35 (62%)
Query: 279 IAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIG 313
+ ++ + +L + +LQ + GREPT E A+A+G
Sbjct: 282 VHMVETINKLSRTARQLQQELGREPTYEEIAEAMG 316
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 37/66 (56%), Gaps = 6/66 (9%)
Query: 316 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQATFNFGKW 371
+D+ + G + ++++++ ANLRLV+ +AK+Y RG+ DL+Q + K
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ--EGNIGLMKA 415
Query: 372 LLLFQY 377
+ F+Y
Sbjct: 416 VDKFEY 421
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 613
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 37/66 (56%), Gaps = 6/66 (9%)
Query: 316 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQATFNFGKW 371
+D+ + G + ++++++ ANLRLV+ +AK+Y RG+ DL+Q + K
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ--EGNIGLMKA 415
Query: 372 LLLFQY 377
+ F+Y
Sbjct: 416 VDKFEY 421
>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
Escherichia Coli Rna Polymerase
Length = 339
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 31/49 (63%), Gaps = 4/49 (8%)
Query: 316 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
+D+ + G + ++++++ ANLRLV+ +AK+Y RG+ DL+Q
Sbjct: 249 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 297
>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 = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 25/43 (58%)
Query: 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSS 329
R+++ KL+ + GREPT E AK +G+S +L L N S
Sbjct: 100 RIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFS 142
>pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti-
Sigma Factor Spoiiab With The Sporulation Sigma Factor
Sigmaf
Length = 243
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQVN 362
+R+++I N+RLV V +++ RG DL Q+
Sbjct: 29 ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIG 62
>pdb|3HV0|A Chain A, Tryptophanyl-Trna Synthetase From Cryptosporidium Parvum
pdb|3HV0|B Chain B, Tryptophanyl-Trna Synthetase From Cryptosporidium Parvum
Length = 393
Score = 28.9 bits (63), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 46/94 (48%), Gaps = 17/94 (18%)
Query: 210 FSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKL 269
F P ++ ++ + K +T ET+N ++K ++ GFD PE +
Sbjct: 106 FKVPLVIQLTDDEKFIFKSNLTLEETHNYAYENMKDIIACGFD-----------PELTFI 154
Query: 270 LTADEEFELIAQIQ-DLIRLEKE--KSKLQSQFG 300
T E IA++ D++R+EK+ S+++S FG
Sbjct: 155 FT---NLEYIAELYPDILRIEKKISCSQIKSIFG 185
>pdb|3IKM|A Chain A, Crystal Structure Of Human Mitochondrial Dna Polymerase
Holoenzyme
pdb|3IKM|D Chain D, Crystal Structure Of Human Mitochondrial Dna Polymerase
Holoenzyme
Length = 1172
Score = 28.5 bits (62), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 20/39 (51%)
Query: 273 DEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKA 311
D+ F L+AQ Q L LE LQ+Q +P WA+
Sbjct: 67 DQHFRLLAQKQSLPYLEAANLLLQAQLPPKPPAWAWAEG 105
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 0.131 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,268,363
Number of Sequences: 62578
Number of extensions: 325228
Number of successful extensions: 921
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: 887
Number of HSP's gapped (non-prelim): 35
length of query: 378
length of database: 14,973,337
effective HSP length: 100
effective length of query: 278
effective length of database: 8,715,537
effective search space: 2422919286
effective search space used: 2422919286
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: 52 (24.6 bits)