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= 026599
(236 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1AM9|A Chain A, Human Srebp-1a Bound To Ldl Receptor Promoter
pdb|1AM9|B Chain B, Human Srebp-1a Bound To Ldl Receptor Promoter
pdb|1AM9|C Chain C, Human Srebp-1a Bound To Ldl Receptor Promoter
pdb|1AM9|D Chain D, Human Srebp-1a Bound To Ldl Receptor Promoter
Length = 82
Score = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 1/69 (1%)
Query: 84 EKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEK 143
EK R +NDK +EL ++ G K +K+A+L A+ + L+ QKLK N SL+
Sbjct: 14 EKRYRSSINDKIIELKDLV-VGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA 72
Query: 144 IKELKAEKN 152
+ + K+ K+
Sbjct: 73 VHKSKSLKD 81
>pdb|2I1J|A Chain A, Moesin From Spodoptera Frugiperda At 2.1 Angstroms
Resolution
pdb|2I1K|A Chain A, Moesin From Spodoptera Frugiperda Reveals The Coiled-Coil
Domain At 3.0 Angstrom Resolution
Length = 575
Score = 32.3 bits (72), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 28/106 (26%), Positives = 53/106 (50%), Gaps = 5/106 (4%)
Query: 80 KACREKLR-----RDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLK 134
+A REKL+ R+R K E L + A L++A M+ +L + ++L+
Sbjct: 317 QAQREKLQLEIAARERAEKKQQEYQDRLRQMQEEMERSQANLLEAQDMILRLEEQLRQLQ 376
Query: 135 DSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQPS 180
+ L+++ EL+A L + K AE++K+E +++A + S
Sbjct: 377 AAKEELEQRQNELQAMMQRLEETKNMEAAERQKLEDEIRAKQEEVS 422
>pdb|1QVR|A Chain A, Crystal Structure Analysis Of Clpb
pdb|1QVR|B Chain B, Crystal Structure Analysis Of Clpb
pdb|1QVR|C Chain C, Crystal Structure Analysis Of Clpb
Length = 854
Score = 31.6 bits (70), Expect = 0.42, Method: Composition-based stats.
Identities = 27/88 (30%), Positives = 46/88 (52%), Gaps = 2/88 (2%)
Query: 90 RLNDKFVELASILEPGRPPKTDKAAILIDAV-RMVTQLRSEAQKLK-DSNSSLQEKIKEL 147
RL DK ++L + A IDA+ R QL E + LK + + QE++K +
Sbjct: 376 RLPDKAIDLIDEAAARLRMALESAPEEIDALERKKLQLEIEREALKKEKDPDSQERLKAI 435
Query: 148 KAEKNELRDEKQRLKAEKEKIEQQLKAM 175
+AE +L +E +L+AE E+ + L+ +
Sbjct: 436 EAEIAKLTEEIAKLRAEWEREREILRKL 463
>pdb|2JEE|A Chain A, Xray Structure Of E. Coli Yiiu
pdb|2JEE|B Chain B, Xray Structure Of E. Coli Yiiu
pdb|2JEE|C Chain C, Xray Structure Of E. Coli Yiiu
pdb|2JEE|D Chain D, Xray Structure Of E. Coli Yiiu
Length = 81
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 37/57 (64%)
Query: 119 AVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM 175
A+ +T L+ E ++LK+ N+SL ++++ + ++ EL E LK ++ +++L+A+
Sbjct: 18 AIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQAL 74
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1118
Score = 28.1 bits (61), Expect = 4.3, Method: Composition-based stats.
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 90 RLNDKFVELASILEPGRPPKTDKA 113
R + V L ++L PG PPK DKA
Sbjct: 230 RPEEAMVRLFTLLRPGDPPKKDKA 253
>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 = 28.1 bits (61), Expect = 4.3, Method: Composition-based stats.
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 90 RLNDKFVELASILEPGRPPKTDKA 113
R + V L ++L PG PPK DKA
Sbjct: 230 RPEEAMVRLFTLLRPGDPPKKDKA 253
>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 = 28.1 bits (61), Expect = 4.3, Method: Composition-based stats.
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 90 RLNDKFVELASILEPGRPPKTDKA 113
R + V L ++L PG PPK DKA
Sbjct: 230 RPEEAMVRLFTLLRPGDPPKKDKA 253
>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 = 28.1 bits (61), Expect = 4.3, Method: Composition-based stats.
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 90 RLNDKFVELASILEPGRPPKTDKA 113
R + V L ++L PG PPK DKA
Sbjct: 230 RPEEAMVRLFTLLRPGDPPKKDKA 253
>pdb|2QAG|C Chain C, Crystal Structure Of Human Septin Trimer 267
Length = 418
Score = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 11/58 (18%)
Query: 125 QLRSEAQKLKDSNSSLQEKI-----------KELKAEKNELRDEKQRLKAEKEKIEQQ 171
+++ + QKLKDS + LQ + KEL+ ++ + DEK +A++ +EQQ
Sbjct: 345 KVKEKVQKLKDSEAELQRRHEQMKKNLEAQHKELEEKRRQFEDEKANWEAQQRILEQQ 402
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 27.7 bits (60), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 84 EKLRRDRLNDKFVELASILEP--GRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSN 137
EK RRD++N ELAS++ K DK +L AV+ + LR ++N
Sbjct: 21 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYTEAN 76
>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 = 27.7 bits (60), Expect = 6.0, Method: Composition-based stats.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 90 RLNDKFVELASILEPGRPPKTDKA 113
R + + L ++L PG PPK DKA
Sbjct: 230 RPEEALIRLFTLLRPGDPPKRDKA 253
>pdb|3M9H|A Chain A, Crystal Structure Of The Amino Terminal Coiled Coil Domain
Of The Mycobacterium Tuberculosis Proteasomal Atpase Mpa
pdb|3M9H|B Chain B, Crystal Structure Of The Amino Terminal Coiled Coil Domain
Of The Mycobacterium Tuberculosis Proteasomal Atpase Mpa
pdb|3M9H|C Chain C, Crystal Structure Of The Amino Terminal Coiled Coil Domain
Of The Mycobacterium Tuberculosis Proteasomal Atpase Mpa
pdb|3M9H|D Chain D, Crystal Structure Of The Amino Terminal Coiled Coil Domain
Of The Mycobacterium Tuberculosis Proteasomal Atpase Mpa
pdb|3M9H|E Chain E, Crystal Structure Of The Amino Terminal Coiled Coil Domain
Of The Mycobacterium Tuberculosis Proteasomal Atpase Mpa
pdb|3M9H|F Chain F, Crystal Structure Of The Amino Terminal Coiled Coil Domain
Of The Mycobacterium Tuberculosis Proteasomal Atpase Mpa
Length = 55
Score = 26.9 bits (58), Expect = 8.8, Method: Composition-based stats.
Identities = 15/43 (34%), Positives = 22/43 (51%)
Query: 119 AVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRL 161
+ R + QL + L NS L E +KE + + LR+E RL
Sbjct: 11 SARDIHQLEARIDSLAARNSKLMETLKEARQQLLALREEVDRL 53
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
0.314 0.131 0.378
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,920,078
Number of Sequences: 62578
Number of extensions: 193264
Number of successful extensions: 789
Number of sequences better than 100.0: 65
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 35
Number of HSP's that attempted gapping in prelim test: 712
Number of HSP's gapped (non-prelim): 100
length of query: 236
length of database: 14,973,337
effective HSP length: 96
effective length of query: 140
effective length of database: 8,965,849
effective search space: 1255218860
effective search space used: 1255218860
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)