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= 017772
(366 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3HSU|A Chain A, Functional Roles Of The 6-S-Cysteinyl, 8 Alpha-N1-Histidyl
Fad In Glucooligosaccharide Oxidase From Acremonium
Strictum
Length = 503
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 11 IEVSKEKDPDLFYLARCGLGGLGVVAEVTLQCVERQELV 49
+ VS+ ++ DLF+ R G GG +V+E E E++
Sbjct: 177 VHVSETENADLFWALRGGGGGFAIVSEFEFNTFEAPEII 215
>pdb|1ZR6|A Chain A, The Crystal Structure Of An Acremonium Strictum
Glucooligosaccharide Oxidase Reveals A Novel
Flavinylation
pdb|2AXR|A Chain A, Crystal Structure Of Glucooligosaccharide Oxidase From
Acremonium Strictum: A Novel Flavinylation Of
6-S-Cysteinyl, 8alpha-N1-Histidyl Fad
Length = 503
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 11 IEVSKEKDPDLFYLARCGLGGLGVVAEVTLQCVERQELV 49
+ VS+ ++ DLF+ R G GG +V+E E E++
Sbjct: 177 VHVSETENADLFWALRGGGGGFAIVSEFEFNTFEAPEII 215
>pdb|2GK4|A Chain A, The Crystal Structure Of The Dna/pantothenate Metabolism
Flavoprotein From Streptococcus Pneumoniae
pdb|2GK4|B Chain B, The Crystal Structure Of The Dna/pantothenate Metabolism
Flavoprotein From Streptococcus Pneumoniae
Length = 232
Score = 32.3 bits (72), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 46/100 (46%), Gaps = 9/100 (9%)
Query: 55 SNIKEI--KKNHKKLLSENKHVKYLHIPYTDTVVVVTC--NPVSKWKGPLKFKPKYTKDE 110
SN+KE K+NH+ +S V+ L + T ++ + NP G K T+D
Sbjct: 112 SNLKEFLSKQNHQAKISSTDEVQVLFLKKTPKIISLVKEWNPTIHLIG-FKLLVDVTED- 169
Query: 111 ALQHLRDLYRESLKKYRADVMTAKSPDGTEPDINELSFTE 150
HL D+ R+SL K +AD++ A D + F E
Sbjct: 170 ---HLVDIARKSLIKNQADLIIANDLTQISADQHRAIFVE 206
>pdb|4EGY|A Chain A, Crystal Structure Of Arar(dbd) In Complex With Operator
Ora1
pdb|4EGY|B Chain B, Crystal Structure Of Arar(dbd) In Complex With Operator
Ora1
pdb|4EGZ|A Chain A, Crystal Structure Of Arar(dbd) In Complex With Operator
Orr3
pdb|4EGZ|B Chain B, Crystal Structure Of Arar(dbd) In Complex With Operator
Orr3
pdb|4H0E|A Chain A, Crystal Structure Of Mutant Orr3 In Complex With Ntd Of
Arar
pdb|4H0E|B Chain B, Crystal Structure Of Mutant Orr3 In Complex With Ntd Of
Arar
Length = 88
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 25/53 (47%)
Query: 253 MSPAYSSVQDDIFSWVGIIMYLPTMDARQRKEITDEFFNYRHLSQKQLWDQYS 305
M P Y+ V+++I SW+ LP E+ +F RH +K + D S
Sbjct: 21 MLPKYAQVKEEISSWINQGKILPDQKIPTENELMQQFGVSRHTIRKAIGDLVS 73
>pdb|1IW7|C Chain C, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|M Chain M, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|C Chain C, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|M Chain M, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|C Chain C, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|M Chain M, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|2A68|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|C Chain C, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|M Chain M, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2O5I|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5I|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5J|C Chain C, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2O5J|M Chain M, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2PPB|C Chain C, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|2PPB|M Chain M, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|3DXJ|C Chain C, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|M Chain M, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3EQL|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3AOH|C Chain C, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|H Chain H, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|M Chain M, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOI|C Chain C, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|H Chain H, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|M Chain M, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|4G7H|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4GZY|C Chain C, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
pdb|4GZZ|C Chain C, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
Length = 1119
Score = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 303 QYSAYEHWAKIEVPKDKEELAALQARLRKRFPVDSYNKARKEL 345
Q +Y + +VP +K E +QA R+ FP++ +K + L
Sbjct: 22 QVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGL 64
>pdb|3MLQ|A Chain A, Crystal Structure Of The Thermus Thermophilus
Transcription-Repair Coupling Factor Rna Polymerase
Interacting Domain With The Thermus Aquaticus Rna
Polymerase Beta1 Domain
pdb|3MLQ|B Chain B, Crystal Structure Of The Thermus Thermophilus
Transcription-Repair Coupling Factor Rna Polymerase
Interacting Domain With The Thermus Aquaticus Rna
Polymerase Beta1 Domain
pdb|3MLQ|C Chain C, Crystal Structure Of The Thermus Thermophilus
Transcription-Repair Coupling Factor Rna Polymerase
Interacting Domain With The Thermus Aquaticus Rna
Polymerase Beta1 Domain
pdb|3MLQ|D Chain D, Crystal Structure Of The Thermus Thermophilus
Transcription-Repair Coupling Factor Rna Polymerase
Interacting Domain With The Thermus Aquaticus Rna
Polymerase Beta1 Domain
Length = 188
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 12/43 (27%), Positives = 24/43 (55%)
Query: 303 QYSAYEHWAKIEVPKDKEELAALQARLRKRFPVDSYNKARKEL 345
Q +Y+ + +VP +K E +QA ++ FP++ +K + L
Sbjct: 7 QVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGL 49
>pdb|1YNJ|C Chain C, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|C Chain C, Taq Rna Polymerase-rifampicin Complex
pdb|2GHO|C Chain C, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1119
Score = 29.3 bits (64), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 12/43 (27%), Positives = 24/43 (55%)
Query: 303 QYSAYEHWAKIEVPKDKEELAALQARLRKRFPVDSYNKARKEL 345
Q +Y+ + +VP +K E +QA ++ FP++ +K + L
Sbjct: 22 QVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGL 64
>pdb|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|L Chain L, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|C Chain C, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 1118
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 12/43 (27%), Positives = 24/43 (55%)
Query: 303 QYSAYEHWAKIEVPKDKEELAALQARLRKRFPVDSYNKARKEL 345
Q +Y+ + +VP +K E +QA ++ FP++ +K + L
Sbjct: 22 QVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGL 64
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1118
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 12/43 (27%), Positives = 24/43 (55%)
Query: 303 QYSAYEHWAKIEVPKDKEELAALQARLRKRFPVDSYNKARKEL 345
Q +Y+ + +VP +K E +QA ++ FP++ +K + L
Sbjct: 22 QVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGL 64
>pdb|1HQM|C Chain C, Crystal Structure Of Thermus Aquaticus Core Rna
Polymerase- Includes Complete Structure With Side-Chains
(Except For Disordered Regions)-Further Refined From
Original Deposition-Contains Additional Sequence
Information
Length = 1119
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 12/43 (27%), Positives = 24/43 (55%)
Query: 303 QYSAYEHWAKIEVPKDKEELAALQARLRKRFPVDSYNKARKEL 345
Q +Y+ + +VP +K E +QA ++ FP++ +K + L
Sbjct: 22 QVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGL 64
>pdb|4ETP|B Chain B, C-Terminal Motor And Motor Homology Domain Of Kar3vik1
Fused To A Synthetic Heterodimeric Coiled Coil
Length = 333
Score = 28.5 bits (62), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 30/47 (63%), Gaps = 2/47 (4%)
Query: 314 EVPKDKEELAALQARLRK--RFPVDSYNKARKELDPNRILSNNMLEK 358
E+ ++E+AAL+ + K +F D+YN KEL +R L N+++E+
Sbjct: 11 EIAALEKEIAALEKEISKQEKFYNDTYNTVCKELLRSRRLENSIIEQ 57
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 0.133 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,271,276
Number of Sequences: 62578
Number of extensions: 470845
Number of successful extensions: 1301
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1289
Number of HSP's gapped (non-prelim): 18
length of query: 366
length of database: 14,973,337
effective HSP length: 100
effective length of query: 266
effective length of database: 8,715,537
effective search space: 2318332842
effective search space used: 2318332842
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)