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= 014241
(428 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 = 107 bits (268), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 66/173 (38%), Positives = 103/173 (59%), Gaps = 22/173 (12%)
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-GSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
DL+Q G+ GL+++VEKF+ + +F++YA WW+RQ I +AI +RTIR+PV
Sbjct: 119 LDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPV 171
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 102 bits (255), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 66/188 (35%), Positives = 103/188 (54%), Gaps = 37/188 (19%)
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-GSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 399
VV +AK+Y GRG+S DL+Q G+ GL+++VEKF+ + +F++YA WW+RQ I +AI
Sbjct: 210 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 269
Query: 400 SRTIRLPV 407
+RTIR+PV
Sbjct: 270 ARTIRIPV 277
>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 = 101 bits (251), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 66/188 (35%), Positives = 103/188 (54%), Gaps = 37/188 (19%)
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-GSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 399
VV +AK+Y GRG+S DL+Q G+ GL+++VEKF+ + +F++YA WW+RQ I +AI
Sbjct: 123 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 182
Query: 400 SRTIRLPV 407
+RTIR+PV
Sbjct: 183 ARTIRIPV 190
>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 = 100 bits (250), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 66/188 (35%), Positives = 103/188 (54%), Gaps = 37/188 (19%)
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---SGNSSREKLINANLRL 340
+G + ++LK LH G ++R+ LI ANLRL
Sbjct: 59 ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 118
Query: 341 VVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 399
VV +AK+Y GRG+S DL+Q G+ GL+++VEKF+ + +F++YA WW+RQ I +AI
Sbjct: 119 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 178
Query: 400 SRTIRLPV 407
+RTIR+PV
Sbjct: 179 ARTIRIPV 186
>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 = 99.8 bits (247), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 44/83 (53%), Positives = 64/83 (77%), Gaps = 1/83 (1%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYA 384
G ++R+ LI ANLRLVV +AK+Y GRG+S DL+Q G+ GL+++VEKF+ + +F++YA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 385 YWWVRQTIRKAIFQHSRTIRLPV 407
WW+RQ I +AI +RTIR+PV
Sbjct: 240 TWWIRQAINRAIADQARTIRIPV 262
>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 = 99.8 bits (247), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 44/83 (53%), Positives = 64/83 (77%), Gaps = 1/83 (1%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYA 384
G ++R+ LI ANLRLVV +AK+Y GRG+S DL+Q G+ GL+++VEKF+ + +F++YA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 385 YWWVRQTIRKAIFQHSRTIRLPV 407
WW+RQ I +AI +RTIR+PV
Sbjct: 240 TWWIRQAINRAIADQARTIRIPV 262
>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 = 99.4 bits (246), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 44/83 (53%), Positives = 64/83 (77%), Gaps = 1/83 (1%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYA 384
G ++R+ LI ANLRLVV +AK+Y GRG+S DL+Q G+ GL+++VEKF+ + +F++YA
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 259
Query: 385 YWWVRQTIRKAIFQHSRTIRLPV 407
WW+RQ I +AI +RTIR+PV
Sbjct: 260 TWWIRQAINRAIADQARTIRIPV 282
Score = 28.1 bits (61), Expect = 9.6, 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 = 94.4 bits (233), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 40/97 (41%), Positives = 69/97 (71%), Gaps = 5/97 (5%)
Query: 316 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVE 370
+D+ + G + ++++++ ANLRLV+ +AK+Y RG+ DL+Q G++GLMK+V+
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 417
Query: 371 KFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
KF+ + G +F++YA WW+RQ I ++I +RTIR+PV
Sbjct: 418 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 454
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 613
Score = 94.4 bits (233), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 40/97 (41%), Positives = 69/97 (71%), Gaps = 5/97 (5%)
Query: 316 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVE 370
+D+ + G + ++++++ ANLRLV+ +AK+Y RG+ DL+Q G++GLMK+V+
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 417
Query: 371 KFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
KF+ + G +F++YA WW+RQ I ++I +RTIR+PV
Sbjct: 418 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 454
>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 = 91.7 bits (226), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 44/89 (49%), Positives = 64/89 (71%), Gaps = 4/89 (4%)
Query: 317 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKF 372
++LK LH G ++R+ LI ANLRLVV +AK+Y GRG+S DL+Q G+ GL+++VEKF
Sbjct: 91 KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 150
Query: 373 KPQAGCRFASYAYWWVRQTIRKAIFQHSR 401
+ + G F++YA WW+RQ I +AI +R
Sbjct: 151 EYKRGFAFSTYATWWIRQAINRAIADQAR 179
>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
Escherichia Coli Rna Polymerase
Length = 339
Score = 81.6 bits (200), Expect = 7e-16, Method: Compositional matrix adjust.
Identities = 35/91 (38%), Positives = 63/91 (69%), Gaps = 5/91 (5%)
Query: 316 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVE 370
+D+ + G + ++++++ ANLRLV+ +AK+Y RG+ DL+Q G++GLMK+V+
Sbjct: 249 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 308
Query: 371 KFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 401
KF+ + G +F++YA WW+RQ I ++I +R
Sbjct: 309 KFEYRRGYKFSTYATWWIRQAITRSIADQAR 339
>pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti-
Sigma Factor Spoiiab With The Sporulation Sigma Factor
Sigmaf
Length = 243
Score = 48.1 bits (113), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYA 384
+R+++I N+RLV V +++ RG DL Q G +GL+KSV+KF +F++YA
Sbjct: 29 ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYA 85
>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 = 30.4 bits (67), Expect = 1.9, 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|3HV0|A Chain A, Tryptophanyl-Trna Synthetase From Cryptosporidium Parvum
pdb|3HV0|B Chain B, Tryptophanyl-Trna Synthetase From Cryptosporidium Parvum
Length = 393
Score = 28.5 bits (62), Expect = 7.1, 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 = 7.5, 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
0.317 0.132 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,476,960
Number of Sequences: 62578
Number of extensions: 376060
Number of successful extensions: 1232
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: 1187
Number of HSP's gapped (non-prelim): 34
length of query: 428
length of database: 14,973,337
effective HSP length: 102
effective length of query: 326
effective length of database: 8,590,381
effective search space: 2800464206
effective search space used: 2800464206
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)