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= 011324
(488 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 = 130 bits (326), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 80/240 (33%), Positives = 138/240 (57%), Gaps = 23/240 (9%)
Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 310
+DP+R +L LLT +EE +L ++++ I+ E + L + RE + AK
Sbjct: 2 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 58
Query: 311 AIGLSC------------RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISL 355
+G + ++LK LH G ++R+ LI ANLRLVV +AK+Y GRG+S
Sbjct: 59 ILGTARVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSF 118
Query: 356 HDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 415
DL+QEG+ GL+++VEKF+ + +F++YA WW+RQ I +AI +RTIR+P ++ ++
Sbjct: 119 LDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETIN 178
Query: 416 KVLEAKRLYIQEGNHSPDKEDLARRVGIT--VEKLERLIFITRMPLSMQQPVWADQDTTF 473
K+ R QE P E++A +G +++E + I + P+S++ P+ ++D+ +
Sbjct: 179 KLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFY 238
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 613
Score = 128 bits (322), Expect = 6e-30, Method: Compositional matrix adjust.
Identities = 57/160 (35%), Positives = 106/160 (66%), Gaps = 4/160 (2%)
Query: 316 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVE 371
+D+ + G + ++++++ ANLRLV+ +AK+Y RG+ DL+QEG++GLMK+V+
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 417
Query: 372 KFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHS 431
KF+ + G +F++YA WW+RQ I ++I +RTIR+P ++ ++K+ R +QE
Sbjct: 418 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 477
Query: 432 PDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT 471
P E+LA R+ + +K+ +++ I + P+SM+ P+ D+D+
Sbjct: 478 PTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS 517
>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 = 128 bits (322), Expect = 6e-30, Method: Compositional matrix adjust.
Identities = 57/160 (35%), Positives = 106/160 (66%), Gaps = 4/160 (2%)
Query: 316 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVE 371
+D+ + G + ++++++ ANLRLV+ +AK+Y RG+ DL+QEG++GLMK+V+
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 417
Query: 372 KFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHS 431
KF+ + G +F++YA WW+RQ I ++I +RTIR+P ++ ++K+ R +QE
Sbjct: 418 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 477
Query: 432 PDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT 471
P E+LA R+ + +K+ +++ I + P+SM+ P+ D+D+
Sbjct: 478 PTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS 517
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 126 bits (316), Expect = 3e-29, Method: Compositional matrix adjust.
Identities = 80/255 (31%), Positives = 138/255 (54%), Gaps = 38/255 (14%)
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 VVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 400
VV +AK+Y GRG+S DL+QEG+ GL+++VEKF+ + +F++YA WW+RQ I +AI
Sbjct: 210 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 269
Query: 401 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGIT--VEKLERLIFITRMP 458
+RTIR+P ++ ++K+ R QE P E++A +G +++E + I + P
Sbjct: 270 ARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEP 329
Query: 459 LSMQQPVWADQDTTF 473
+S++ P+ ++D+ +
Sbjct: 330 VSLETPIGDEKDSFY 344
>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 = 124 bits (311), Expect = 1e-28, Method: Compositional matrix adjust.
Identities = 63/165 (38%), Positives = 106/165 (64%), Gaps = 5/165 (3%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 385
G ++R+ LI ANLRLVV +AK+Y GRG+S DL+QEG+ GL+++VEKF+ + +F++YA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 386 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGIT- 444
WW+RQ I +AI +RTIR+P ++ ++K+ R QE P E++A +G
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 445 -VEKLERLIFITRMPLSMQQPVWADQDTTF-QVMPLLLSHLPSDI 487
+++E + I + P+S++ P+ ++D+ + +P HLPS +
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIP--DEHLPSPV 342
>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 = 124 bits (311), Expect = 1e-28, Method: Compositional matrix adjust.
Identities = 63/165 (38%), Positives = 106/165 (64%), Gaps = 5/165 (3%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 385
G ++R+ LI ANLRLVV +AK+Y GRG+S DL+QEG+ GL+++VEKF+ + +F++YA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 386 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGIT- 444
WW+RQ I +AI +RTIR+P ++ ++K+ R QE P E++A +G
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 445 -VEKLERLIFITRMPLSMQQPVWADQDTTF-QVMPLLLSHLPSDI 487
+++E + I + P+S++ P+ ++D+ + +P HLPS +
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIP--DEHLPSPV 342
>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 = 124 bits (310), Expect = 1e-28, Method: Compositional matrix adjust.
Identities = 63/165 (38%), Positives = 106/165 (64%), Gaps = 5/165 (3%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 385
G ++R+ LI ANLRLVV +AK+Y GRG+S DL+QEG+ GL+++VEKF+ + +F++YA
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 259
Query: 386 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGIT- 444
WW+RQ I +AI +RTIR+P ++ ++K+ R QE P E++A +G
Sbjct: 260 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 319
Query: 445 -VEKLERLIFITRMPLSMQQPVWADQDTTF-QVMPLLLSHLPSDI 487
+++E + I + P+S++ P+ ++D+ + +P HLPS +
Sbjct: 320 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIP--DEHLPSPV 362
>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 = 116 bits (291), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 60/150 (40%), Positives = 97/150 (64%), Gaps = 5/150 (3%)
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 KPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPD 433
+ + +F++YA WW+RQ I +AI +RTIR+P ++ ++K+ R QE P
Sbjct: 152 EYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPS 211
Query: 434 KEDLARRVGIT--VEKLERLIFITRMPLSM 461
E++A +G +++E + I + P+S+
Sbjct: 212 YEEIAEAMGPGWDAKRVEETLKIAQEPVSL 241
>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 = 116 bits (291), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 60/150 (40%), Positives = 97/150 (64%), Gaps = 5/150 (3%)
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 KPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPD 433
+ + +F++YA WW+RQ I +AI +RTIR+P ++ ++K+ R QE P
Sbjct: 156 EYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPS 215
Query: 434 KEDLARRVGIT--VEKLERLIFITRMPLSM 461
E++A +G +++E + I + P+S+
Sbjct: 216 YEEIAEAMGPGWDAKRVEETLKIAQEPVSL 245
>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 = 98.6 bits (244), Expect = 8e-21, Method: Compositional matrix adjust.
Identities = 45/89 (50%), Positives = 65/89 (73%), Gaps = 3/89 (3%)
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 KPQAGCRFASYAYWWVRQTIRKAIFQHSR 402
+ + 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 = 88.2 bits (217), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 34/74 (45%), Positives = 58/74 (78%)
Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388
++++++ ANLRLV+ +AK+Y RG+ DL+QEG++GLMK+V+KF+ + G +F++YA WW
Sbjct: 266 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 325
Query: 389 VRQTIRKAIFQHSR 402
+RQ I ++I +R
Sbjct: 326 IRQAITRSIADQAR 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 = 63.2 bits (152), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 37/138 (26%), Positives = 75/138 (54%), Gaps = 1/138 (0%)
Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388
+R+++I N+RLV V +++ RG DL Q G +GL+KSV+KF +F++YA
Sbjct: 29 ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPM 88
Query: 389 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 448
+ I++ + T+++ ++ + +K+ +AK + +P ++A +GI+ E +
Sbjct: 89 IIGEIQR-FLRDDGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDV 147
Query: 449 ERLIFITRMPLSMQQPVW 466
R+P S+ + V+
Sbjct: 148 VLAQEAVRLPTSIHETVY 165
>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 = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 35/135 (25%), Positives = 67/135 (49%), Gaps = 20/135 (14%)
Query: 324 HSGNSSREKLINANLRLVVHVA---KQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCR 380
+S RE+LI L LV +A K++ + + DL+ G +GL+K+V+ + R
Sbjct: 8 YSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKR 67
Query: 381 FASYAYWWVRQTIRKAIFQH-------SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPD 433
A +++ I+ AI+ + SR +R E + +V+E + ++ P
Sbjct: 68 ----AEAYIKLRIKGAIYDYLRSLDFGSRQVREKER---RIKEVVEKLK---EKLGREPT 117
Query: 434 KEDLARRVGITVEKL 448
E++A+ +GI+ E+L
Sbjct: 118 DEEVAKELGISTEEL 132
Score = 30.4 bits (67), Expect = 2.4, 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|3MZY|A Chain A, The Crystal Structure Of The Rna Polymerase Sigma-H Factor
F Fusobacterium Nucleatum To 2.5a
Length = 164
Score = 37.7 bits (86), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 30/49 (61%), Gaps = 5/49 (10%)
Query: 352 GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ----TIRKA 396
G DL+QEG +GL+K++ KF + F+S+A+ +R+ IRKA
Sbjct: 1 GAEKEDLVQEGILGLLKAI-KFYDETKSSFSSFAFLCIRREXISAIRKA 48
>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 = 7.7, 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 = 8.3, 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
0.316 0.132 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,275,751
Number of Sequences: 62578
Number of extensions: 448903
Number of successful extensions: 1460
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1422
Number of HSP's gapped (non-prelim): 37
length of query: 488
length of database: 14,973,337
effective HSP length: 103
effective length of query: 385
effective length of database: 8,527,803
effective search space: 3283204155
effective search space used: 3283204155
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)