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= 011992
(473 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 = 75.9 bits (185), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 52/148 (35%), Positives = 84/148 (56%), Gaps = 21/148 (14%)
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 HDLLQEGSMGLMKSVEKFKPQAGCRFAN 383
DL+QEG+ GL+++VEKF+ + +F+
Sbjct: 119 LDLIQEGNQGLIRAVEKFEYKRRFKFST 146
Score = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 47/69 (68%)
Query: 389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 448
P + + L+ + + L+ L+ +E +++LR G+ DG+ +L EVG FG+++ER+RQ+
Sbjct: 250 PVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQI 309
Query: 449 ESRALYRLK 457
E++AL +LK
Sbjct: 310 ENKALRKLK 318
>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 = 72.4 bits (176), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 35/70 (50%), Positives = 51/70 (72%), Gaps = 3/70 (4%)
Query: 317 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 373
++LK LH G ++R+ LI ANLRLVV +AK+Y GRG+S DL+QEG+ GL+++VEKF
Sbjct: 91 KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 150
Query: 374 KPQAGCRFAN 383
+ + G F+
Sbjct: 151 EYKRGFAFST 160
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 70.9 bits (172), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 52/163 (31%), Positives = 84/163 (51%), Gaps = 36/163 (22%)
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 VVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN 383
VV +AK+Y GRG+S DL+QEG+ GL+++VEKF+ + +F+
Sbjct: 210 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST 252
Score = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 47/69 (68%)
Query: 389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 448
P + + L+ + + L+ L+ +E +++LR G+ DG+ +L EVG FG+++ER+RQ+
Sbjct: 356 PVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQI 415
Query: 449 ESRALYRLK 457
E++AL +LK
Sbjct: 416 ENKALRKLK 424
>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 = 70.5 bits (171), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 34/70 (48%), Positives = 51/70 (72%), Gaps = 3/70 (4%)
Query: 317 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 373
++LK LH G ++R+ LI ANLRLVV +AK+Y GRG+S DL+QEG+ GL+++VEKF
Sbjct: 92 KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 151
Query: 374 KPQAGCRFAN 383
+ + +F+
Sbjct: 152 EYKRRFKFST 161
>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 = 70.1 bits (170), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 34/70 (48%), Positives = 51/70 (72%), Gaps = 3/70 (4%)
Query: 317 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 373
++LK LH G ++R+ LI ANLRLVV +AK+Y GRG+S DL+QEG+ GL+++VEKF
Sbjct: 96 KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 155
Query: 374 KPQAGCRFAN 383
+ + +F+
Sbjct: 156 EYKRRFKFST 165
>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 = 68.2 bits (165), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 30/58 (51%), Positives = 45/58 (77%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN 383
G ++R+ LI ANLRLVV +AK+Y GRG+S DL+QEG+ GL+++VEKF+ + +F+
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST 237
Score = 55.1 bits (131), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 47/69 (68%)
Query: 389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 448
P + + L+ + + L+ L+ +E +++LR G+ DG+ +L EVG FG+++ER+RQ+
Sbjct: 341 PVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQI 400
Query: 449 ESRALYRLK 457
E++AL +LK
Sbjct: 401 ENKALRKLK 409
>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 = 68.2 bits (165), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 30/58 (51%), Positives = 45/58 (77%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN 383
G ++R+ LI ANLRLVV +AK+Y GRG+S DL+QEG+ GL+++VEKF+ + +F+
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST 237
Score = 55.1 bits (131), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 47/69 (68%)
Query: 389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 448
P + + L+ + + L+ L+ +E +++LR G+ DG+ +L EVG FG+++ER+RQ+
Sbjct: 341 PVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQI 400
Query: 449 ESRALYRLK 457
E++AL +LK
Sbjct: 401 ENKALRKLK 409
>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 = 68.2 bits (165), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 30/58 (51%), Positives = 45/58 (77%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN 383
G ++R+ LI ANLRLVV +AK+Y GRG+S DL+QEG+ GL+++VEKF+ + +F+
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST 257
Score = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 47/69 (68%)
Query: 389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 448
P + + L+ + + L+ L+ +E +++LR G+ DG+ +L EVG FG+++ER+RQ+
Sbjct: 361 PVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQI 420
Query: 449 ESRALYRLK 457
E++AL +LK
Sbjct: 421 ENKALRKLK 429
>pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga
Maritima
Length = 87
Score = 67.8 bits (164), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 28/64 (43%), Positives = 48/64 (75%)
Query: 395 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 454
+ LMR+ + +L L+P+E ++R+R+G+ DGKPK+L EVG F +++ER+RQ+E +AL
Sbjct: 5 RMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALR 64
Query: 455 RLKQ 458
+L+
Sbjct: 65 KLRH 68
>pdb|4G6D|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex
Length = 73
Score = 65.9 bits (159), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 51/73 (69%)
Query: 398 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457
M++ + ++L L +E ++RLRFG++DG+ ++L EVG +FG+++ER+RQ+E++AL +L+
Sbjct: 1 MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 458 QSLGGKASYGYAD 470
K + D
Sbjct: 61 HPSRSKRLKDFMD 73
>pdb|4G94|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex
Length = 62
Score = 65.5 bits (158), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 48/61 (78%)
Query: 398 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457
M++ + ++L L +E ++RLRFG++DG+ ++L EVG +FG+++ER+RQ+E++AL +L+
Sbjct: 1 MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 458 Q 458
Sbjct: 61 H 61
>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 = 64.3 bits (155), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 50/72 (69%), Gaps = 4/72 (5%)
Query: 316 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVE 371
+D+ + G + ++++++ ANLRLV+ +AK+Y RG+ DL+QEG++GLMK+V+
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 417
Query: 372 KFKPQAGCRFAN 383
KF+ + G +F+
Sbjct: 418 KFEYRRGYKFST 429
Score = 55.5 bits (132), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 49/80 (61%)
Query: 378 GCRFANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNI 437
G +T +E+P S + +R ++L L +E ++R+RFGI+ +L EVG
Sbjct: 520 GDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQ 579
Query: 438 FGLSKERVRQLESRALYRLK 457
F +++ER+RQ+E++AL +L+
Sbjct: 580 FDVTRERIRQIEAKALRKLR 599
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 613
Score = 63.9 bits (154), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 50/72 (69%), Gaps = 4/72 (5%)
Query: 316 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVE 371
+D+ + G + ++++++ ANLRLV+ +AK+Y RG+ DL+QEG++GLMK+V+
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 417
Query: 372 KFKPQAGCRFAN 383
KF+ + G +F+
Sbjct: 418 KFEYRRGYKFST 429
Score = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 49/80 (61%)
Query: 378 GCRFANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNI 437
G +T +E+P S + +R ++L L +E ++R+RFGI+ +L EVG
Sbjct: 520 GDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQ 579
Query: 438 FGLSKERVRQLESRALYRLK 457
F +++ER+RQ+E++AL +L+
Sbjct: 580 FDVTRERIRQIEAKALRKLR 599
>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
Escherichia Coli Rna Polymerase
Length = 339
Score = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 25/55 (45%), Positives = 44/55 (80%)
Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN 383
++++++ ANLRLV+ +AK+Y RG+ DL+QEG++GLMK+V+KF+ + G +F+
Sbjct: 266 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 320
>pdb|1RIO|H Chain H, Structure Of Bacteriophage Lambda Ci-Ntd In Complex With
Sigma-Region4 Of Thermus Aquaticus Bound To Dna
Length = 73
Score = 52.0 bits (123), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 40/52 (76%)
Query: 406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457
L+ L+ +E +++LR G+ DG+ +L EVG FG+++ER+RQ+E++AL +LK
Sbjct: 8 LSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 59
>pdb|1KU3|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
Sigma Subunit Fragment, Region 4
pdb|1KU7|A Chain A, Crystal Structure Of Thermus Aquatics Rna Polymerase
Sigmaa Subunit Region 4 Bound To-35 Element Dna
pdb|1KU7|D Chain D, Crystal Structure Of Thermus Aquatics Rna Polymerase
Sigmaa Subunit Region 4 Bound To-35 Element Dna
Length = 73
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 40/52 (76%)
Query: 406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457
L+ L+ +E ++++R G+ DG+ +L EVG FG+++ER+RQ+E++AL +LK
Sbjct: 8 LSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 59
>pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4
Length = 81
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 42/67 (62%)
Query: 392 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451
S + +R ++L L +E ++R+RFGI+ +L EVG F +++ER+RQ+E++
Sbjct: 2 SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAK 61
Query: 452 ALYRLKQ 458
AL +L+
Sbjct: 62 ALRKLRH 68
>pdb|3T72|QQ Chain q, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|OO Chain o, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
Length = 99
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 42/67 (62%)
Query: 392 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451
S + +R ++L L +E ++R+RFGI+ +L EVG F +++ER+RQ+E++
Sbjct: 3 SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAK 62
Query: 452 ALYRLKQ 458
AL +L+
Sbjct: 63 ALRKLRH 69
>pdb|3N97|A Chain A, Rna Polymerase Alpha C-Terminal Domain (E. Coli) And Sigma
Region 4 (T. Aq. Mutant) Bound To (Up,-35 Element) Dna
pdb|3N97|D Chain D, Rna Polymerase Alpha C-Terminal Domain (E. Coli) And Sigma
Region 4 (T. Aq. Mutant) Bound To (Up,-35 Element) Dna
Length = 72
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 40/53 (75%)
Query: 406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458
L+ L+ +E ++++R G+ DG+ +L EVG FG+++ER+RQ+E++AL +L+
Sbjct: 8 LSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLRH 60
>pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti-
Sigma Factor Spoiiab With The Sporulation Sigma Factor
Sigmaf
Length = 243
Score = 48.9 bits (115), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 35/58 (60%)
Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGV 386
+R+++I N+RLV V +++ RG DL Q G +GL+KSV+KF +F+ V
Sbjct: 29 ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAV 86
Score = 28.5 bits (62), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 30/49 (61%), Gaps = 4/49 (8%)
Query: 409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457
L+ +ER IV LR+ K ++ SEV + G+S+ ++ +LE + L +K
Sbjct: 199 LDERERLIVYLRYY----KDQTQSEVASRLGISQVQMSRLEKKILQHIK 243
>pdb|2P7V|B Chain B, Crystal Structure Of The Escherichia Coli Regulator Of
Sigma 70, Rsd, In Complex With Sigma 70 Domain 4
Length = 68
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 38/55 (69%)
Query: 404 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458
++L L +E ++R+RFGI+ +L EVG F +++ER+RQ+E++AL +L+
Sbjct: 1 DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRH 55
>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 = 33.5 bits (75), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 45/176 (25%), Positives = 79/176 (44%), Gaps = 38/176 (21%)
Query: 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAK 346
R+++ KL+ + GREPT E AK +G+S +L L N S
Sbjct: 100 RIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFS----------------- 142
Query: 347 QYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNLL 406
+SL ++ ++ + + P ++T VE V K+ + + V+ +
Sbjct: 143 ----YILSLEEVFRD----FARDYSELIP------SSTNVE---EEVIKRELTEKVKEAV 185
Query: 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 462
+ L +E+ +++L F E+ K EV I S RV QL+++AL RL++ L
Sbjct: 186 SKLPEREKLVIQLIF-YEELPAK---EVAKILETSVSRVSQLKAKALERLREMLSN 237
Score = 28.9 bits (63), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 3/51 (5%)
Query: 324 HSGNSSREKLINANLRLVVHVA---KQYQGRGISLHDLLQEGSMGLMKSVE 371
+S RE+LI L LV +A K++ + + DL+ G +GL+K+V+
Sbjct: 8 YSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVD 58
>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 = 29.3 bits (64), Expect = 5.3, 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 = 28.9 bits (63), Expect = 6.1, 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 0.132 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,867,641
Number of Sequences: 62578
Number of extensions: 433347
Number of successful extensions: 1285
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1234
Number of HSP's gapped (non-prelim): 52
length of query: 473
length of database: 14,973,337
effective HSP length: 102
effective length of query: 371
effective length of database: 8,590,381
effective search space: 3187031351
effective search space used: 3187031351
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: 53 (25.0 bits)