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= 026646
(235 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 361
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 30/49 (61%), Gaps = 2/49 (4%)
Query: 83 EKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLR-TEAQ 130
EK RRD+ N ELGSML PG K DK+T+L ++ + + + T AQ
Sbjct: 20 EKKRRDQFNVLIKELGSML-PGNARKMDKSTVLQKSIDFLRKHKETTAQ 67
>pdb|4H10|B Chain B, Intermolecular Recognition Revealed By The Complex
Structure Of Human Clock-bmal1 Basic Helix-loop-helix
Domains With E-box Dna
Length = 71
Score = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 78 SKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQ 124
S+ EK RRD+ N ELGSML PG K DK+T+L ++ + +
Sbjct: 11 SRNKSEKKRRDQFNVLIKELGSML-PGNARKMDKSTVLQKSIDFLRK 56
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 33.5 bits (75), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 83 EKLRRDRLNERFLELGSMLEP--GRPPKTDKATILSDAVQMMEQLRTEAQKLKQSN 136
EK RRD++N EL S++ K DK T+L AVQ M+ LR ++N
Sbjct: 21 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYTEAN 76
>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 = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 39/69 (56%), Gaps = 1/69 (1%)
Query: 83 EKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEK 142
EK R +N++ +EL ++ G K +K+ +L A+ + L+ QKLKQ N +L+
Sbjct: 14 EKRYRSSINDKIIELKDLV-VGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA 72
Query: 143 IKELKAEKN 151
+ + K+ K+
Sbjct: 73 VHKSKSLKD 81
>pdb|4ATI|A Chain A, Mitf:m-Box Complex
pdb|4ATI|B Chain B, Mitf:m-Box Complex
pdb|4ATK|A Chain A, Mitf:e-Box Complex
pdb|4ATK|B Chain B, Mitf:e-Box Complex
Length = 118
Score = 32.0 bits (71), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 12/76 (15%)
Query: 83 EKLRRDRLNERFLELGSMLEPGRPP--KTDKATILSDAVQMMEQLRTEAQ---------- 130
E+ RR +N+R ELG+++ P + +K TIL +V + +L+ E Q
Sbjct: 35 ERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENRQK 94
Query: 131 KLKQSNENLQEKIKEL 146
KL+ +N +L +++EL
Sbjct: 95 KLEHANRHLLLRVQEL 110
>pdb|4H10|A Chain A, Intermolecular Recognition Revealed By The Complex
Structure Of Human Clock-bmal1 Basic Helix-loop-helix
Domains With E-box Dna
Length = 73
Score = 31.6 bits (70), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 83 EKLRRDRLNERFLELGSMLEP--GRPPKTDKATILSDAVQMMEQLR 126
EK RRD++N EL S++ K DK T+L AVQ M+ LR
Sbjct: 17 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 62
>pdb|3U4J|A Chain A, Crystal Structure Of Nad-Dependent Aldehyde Dehydrogenase
From Sinorhizobium Meliloti
pdb|3U4J|B Chain B, Crystal Structure Of Nad-Dependent Aldehyde Dehydrogenase
From Sinorhizobium Meliloti
pdb|3U4J|C Chain C, Crystal Structure Of Nad-Dependent Aldehyde Dehydrogenase
From Sinorhizobium Meliloti
pdb|3U4J|D Chain D, Crystal Structure Of Nad-Dependent Aldehyde Dehydrogenase
From Sinorhizobium Meliloti
Length = 528
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 73 CCVSGSKACREKLRRDRLNERFLELGSMLEPGRP 106
CC+SGS+ ++ RD L ER L++ + G P
Sbjct: 303 CCISGSRLLVQEGIRDALXERLLDISRKVAFGDP 336
>pdb|1UKL|C Chain C, Crystal Structure Of Importin-Beta And Srebp-2 Complex
pdb|1UKL|D Chain D, Crystal Structure Of Importin-Beta And Srebp-2 Complex
pdb|1UKL|E Chain E, Crystal Structure Of Importin-Beta And Srebp-2 Complex
pdb|1UKL|F Chain F, Crystal Structure Of Importin-Beta And Srebp-2 Complex
Length = 61
Score = 28.1 bits (61), Expect = 3.9, Method: Composition-based stats.
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 87 RDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKEL 146
R +N++ +EL ++ G K K+ +L A+ ++ L+ KL+Q N L+ L
Sbjct: 1 RSSINDKIIELKDLVX-GTDAKXHKSGVLRKAIDYIKYLQQVNHKLRQENXVLK-----L 54
Query: 147 KAEKNEL 153
+KN+L
Sbjct: 55 ANQKNKL 61
>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 = 28.1 bits (61), Expect = 4.9, Method: Composition-based stats.
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 89 RLNERFLELGSMLEPGRPPKTDKA 112
R E + L ++L PG PPK DKA
Sbjct: 230 RPEEALIRLFTLLRPGDPPKRDKA 253
>pdb|2YST|A Chain A, Solution Structure Of The Third Cadherin Domain From Human
Protocadherin 7
Length = 119
Score = 27.7 bits (60), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 31/52 (59%), Gaps = 5/52 (9%)
Query: 65 RKRLRSESCCVSGSKACREKLRRDRLNE-RFLELGSMLEPGRPPKTDKATIL 115
R+ LR + SG + ++ R+ +N+ RF + + G+PPKTDKAT++
Sbjct: 61 RRLLRLDET--SGWLSVLHRIDREEVNQLRFTVMAR--DRGQPPKTDKATVV 108
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 27.3 bits (59), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 29/106 (27%), Positives = 49/106 (46%), Gaps = 11/106 (10%)
Query: 73 CCVSGSKACREKLRRDRL-NERFLELGS---MLEPGRPPKTDKATILSDAVQMMEQLRTE 128
CC + A + R L +R L LG +LE + D SD+ Q++ +R +
Sbjct: 238 CCAPSNIAVDNLVERLALCKQRILRLGHPARLLESIQQHSLDAVLARSDSAQIVADIRKD 297
Query: 129 AQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 174
++ N+ Q+ K EK+ R+E + L+ KE E++ AM
Sbjct: 298 IDQVFVKNKKTQD-----KREKSNFRNEIKLLR--KELKEREEAAM 336
>pdb|1ZEE|A Chain A, X-Ray Crystal Structure Of Protein So4414 From Shewanella
Oneidensis. Northeast Structural Genomics Consortium
Target Sor52.
pdb|1ZEE|B Chain B, X-Ray Crystal Structure Of Protein So4414 From Shewanella
Oneidensis. Northeast Structural Genomics Consortium
Target Sor52
Length = 403
Score = 26.9 bits (58), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 90 LNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKL 132
+ RF+EL S LE +TD+A + ++ L +E ++L
Sbjct: 15 IRSRFVELNSQLEQLYYQQTDRANVQEVGTELKHTLESEGREL 57
>pdb|4B3G|A Chain A, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
pdb|4B3G|B Chain B, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
Length = 646
Score = 26.9 bits (58), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 29/106 (27%), Positives = 49/106 (46%), Gaps = 11/106 (10%)
Query: 73 CCVSGSKACREKLRRDRL-NERFLELGS---MLEPGRPPKTDKATILSDAVQMMEQLRTE 128
CC + A + R L +R L LG +LE + D SD+ Q++ +R +
Sbjct: 238 CCAPSNIAVDNLVERLALCKQRILRLGHPARLLESIQQHSLDAVLARSDSAQIVADIRKD 297
Query: 129 AQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 174
++ N+ Q+ K EK+ R+E + L+ KE E++ AM
Sbjct: 298 IDQVFVKNKKTQD-----KREKSNFRNEIKLLR--KELKEREEAAM 336
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 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,038,654
Number of Sequences: 62578
Number of extensions: 199039
Number of successful extensions: 908
Number of sequences better than 100.0: 91
Number of HSP's better than 100.0 without gapping: 34
Number of HSP's successfully gapped in prelim test: 57
Number of HSP's that attempted gapping in prelim test: 817
Number of HSP's gapped (non-prelim): 140
length of query: 235
length of database: 14,973,337
effective HSP length: 96
effective length of query: 139
effective length of database: 8,965,849
effective search space: 1246253011
effective search space used: 1246253011
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)