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= 040546
(225 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 42/76 (55%), Gaps = 9/76 (11%)
Query: 50 SKVEAKELAAKK-----HSEAERRRRLRINDQYDNLRKILPNL----VKVDKASVLAKTI 100
++ EA+ LA ++ H+ ERRRR IND+ L ++P ++ +K ++L ++
Sbjct: 14 TESEARALAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASV 73
Query: 101 KTVRELQRTVREQKAL 116
+R+LQR + K L
Sbjct: 74 DYIRKLQREQQRAKDL 89
>pdb|2DLG|A Chain A, Solution Structure Of The 20th Filamin Domain From Human
Filamin-B
Length = 102
Score = 32.0 bits (71), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 154 PEL-MSDLSRALRSVKGRLVRAEMVPVGGRIKCVLWV 189
PE+ SD+S + S GR+ AE+VP+G CV +V
Sbjct: 26 PEINSSDMSAHVTSPSGRVTEAEIVPMGKNSHCVRFV 62
>pdb|2E9I|A Chain A, Solution Structure Of The N-Terminal Extended 20th Filamin
Domain From Human Filamin-B
Length = 106
Score = 32.0 bits (71), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 154 PEL-MSDLSRALRSVKGRLVRAEMVPVGGRIKCVLWV 189
PE+ SD+S + S GR+ AE+VP+G CV +V
Sbjct: 36 PEINSSDMSAHVTSPSGRVTEAEIVPMGKNSHCVRFV 72
>pdb|1R05|A Chain A, Solution Structure Of Max B-Hlh-Lz
pdb|1R05|B Chain B, Solution Structure Of Max B-Hlh-Lz
Length = 87
Score = 31.2 bits (69), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 62 HSEAERRRRLRINDQYDNLRKILPNLV--KVDKASVLAKTIKTVRELQRTV 110
H+ ER+RR I D + +LR +P+L K +A +L K + ++ ++R V
Sbjct: 8 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKV 58
>pdb|1AN4|A Chain A, Structure And Function Of The BHLHZ DOMAIN OF USF
pdb|1AN4|B Chain B, Structure And Function Of The BHLHZ DOMAIN OF USF
Length = 65
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 6/55 (10%)
Query: 61 KHSEAERRRRLRINDQYDNLRKILPNL------VKVDKASVLAKTIKTVRELQRT 109
+H+E ERRRR +IN+ L KI+P+ K +L+K ++EL+++
Sbjct: 8 QHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQS 62
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 58 AAKKHSEAERRRRLRINDQYDNLRKILPNLV----KVDKASVLAKTIKTVRELQ 107
A + HS+ E+RRR ++N D L ++P K+DK +VL ++ ++ L+
Sbjct: 13 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 66
>pdb|1NKP|B Chain B, Crystal Structure Of Myc-Max Recognizing Dna
pdb|1NKP|E Chain E, Crystal Structure Of Myc-Max Recognizing Dna
Length = 83
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 62 HSEAERRRRLRINDQYDNLRKILPNLV--KVDKASVLAKTIKTVRELQR 108
H+ ER+RR I D + +LR +P+L K +A +L K + ++ ++R
Sbjct: 6 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRR 54
>pdb|1NLW|B Chain B, Crystal Structure Of Mad-Max Recognizing Dna
pdb|1NLW|E Chain E, Crystal Structure Of Mad-Max Recognizing Dna
Length = 76
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 62 HSEAERRRRLRINDQYDNLRKILPNLV--KVDKASVLAKTIKTVRELQR 108
H+ ER+RR I D + +LR +P+L K +A +L K + ++ ++R
Sbjct: 5 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRR 53
>pdb|2ZU6|B Chain B, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|E Chain E, Crystal Structure Of The Eif4a-Pdcd4 Complex
Length = 307
Score = 28.5 bits (62), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 152 DQPELMSDLSRALRSVKGRLVRAEMVPVGGRIKCVLWVQGFKGNEGMVMLKRALN 206
D PEL D RA + V + RA VG I C ++ +KG V + AL+
Sbjct: 84 DLPELALDTPRAPQLVGQFIARA----VGDGILCNTYIDSYKGTVDCVQARAALD 134
>pdb|1AN2|A Chain A, Recognition By Max Of Its Cognate Dna Through A Dimeric
BHLHZ DOMAIN
Length = 86
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 62 HSEAERRRRLRINDQYDNLRKILPNLV--KVDKASVLAKTIKTVRELQR 108
H+ ER+RR I D + +LR +P+L K +A +L K + ++ ++R
Sbjct: 7 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRR 55
>pdb|1HLO|A Chain A, The Crystal Structure Of An Intact Human Max-Dna Complex:
New Insights Into Mechanisms Of Transcriptional Control
pdb|1HLO|B Chain B, The Crystal Structure Of An Intact Human Max-Dna Complex:
New Insights Into Mechanisms Of Transcriptional Control
Length = 80
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 51 KVEAKELAAKKHSEAERRRRLRINDQYDNLRKILPNLV--KVDKASVLAKTIKTVRELQR 108
+VE+ H+ ER+RR I D + +LR +P+L K +A +L K + ++ ++R
Sbjct: 5 EVESDADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRR 64
>pdb|3EIQ|C Chain C, Crystal Structure Of Pdcd4-eif4a
Length = 358
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 152 DQPELMSDLSRALRSVKGRLVRAEMVPVGGRIKCVLWVQGFKGNEGMVMLKRALN 206
D PEL D RA + V + RA VG I C ++ +KG V + AL+
Sbjct: 135 DLPELALDTPRAPQLVGQFIARA----VGDGILCNTYIDSYKGTVDCVQARAALD 185
>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 = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 58 AAKKHSEAERRRRLRINDQYDNLRKILPNL----VKVDKASVLAKTIKTVRELQ 107
A + HS+ E+RRR ++N D L ++P K+DK +VL ++ ++ L+
Sbjct: 9 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 62
>pdb|1REQ|A Chain A, Methylmalonyl-Coa Mutase
pdb|1REQ|C Chain C, Methylmalonyl-Coa Mutase
pdb|2REQ|A Chain A, Methylmalonyl-Coa Mutase, Non-Productive Coa Complex, In
Open Conformation Representing Substrate-Free State
pdb|2REQ|C Chain C, Methylmalonyl-Coa Mutase, Non-Productive Coa Complex, In
Open Conformation Representing Substrate-Free State
pdb|3REQ|A Chain A, Methylmalonyl-Coa Mutase, Substrate-Free State (Poor
Quality Structure)
pdb|6REQ|A Chain A, Methylmalonyl-Coa Mutase, 3-Carboxypropyl-Coa Inhibitor
Complex
pdb|6REQ|C Chain C, Methylmalonyl-Coa Mutase, 3-Carboxypropyl-Coa Inhibitor
Complex
pdb|7REQ|A Chain A, Methylmalonyl-Coa Mutase, 2-Carboxypropyl-Coa Inhibitor
Complex
pdb|7REQ|C Chain C, Methylmalonyl-Coa Mutase, 2-Carboxypropyl-Coa Inhibitor
Complex
pdb|4REQ|A Chain A, Methylmalonyl-Coa Mutase Substrate Complex
pdb|4REQ|C Chain C, Methylmalonyl-Coa Mutase Substrate Complex
Length = 727
Score = 28.1 bits (61), Expect = 3.6, Method: Composition-based stats.
Identities = 32/130 (24%), Positives = 58/130 (44%), Gaps = 12/130 (9%)
Query: 45 ISKPISKVEAKELAAKKHSEAERRRRLRINDQYDNLRKILP-NLVKVDKASVLAKTIKTV 103
I K I K+ +E AA+ + + R+ I L P +++KVD ++VLA+ +
Sbjct: 436 IEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKL 495
Query: 104 RELQRTVREQK---ALCQVHEECVFPSEANELSLRNCNRDRGMLKVTLSCEDQPELMSDL 160
+L+ +K AL ++ P + + DR +LK+ + + ++
Sbjct: 496 VKLRAERDPEKVKAALDKITWAAGNPDDKDP--------DRNLLKLCIDAGRAMATVGEM 547
Query: 161 SRALRSVKGR 170
S AL V GR
Sbjct: 548 SDALEKVFGR 557
>pdb|5REQ|A Chain A, Methylmalonyl-Coa Mutase, Y89f Mutant, Substrate Complex
pdb|5REQ|C Chain C, Methylmalonyl-Coa Mutase, Y89f Mutant, Substrate Complex
Length = 727
Score = 28.1 bits (61), Expect = 3.7, Method: Composition-based stats.
Identities = 32/130 (24%), Positives = 58/130 (44%), Gaps = 12/130 (9%)
Query: 45 ISKPISKVEAKELAAKKHSEAERRRRLRINDQYDNLRKILP-NLVKVDKASVLAKTIKTV 103
I K I K+ +E AA+ + + R+ I L P +++KVD ++VLA+ +
Sbjct: 436 IEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKL 495
Query: 104 RELQRTVREQK---ALCQVHEECVFPSEANELSLRNCNRDRGMLKVTLSCEDQPELMSDL 160
+L+ +K AL ++ P + + DR +LK+ + + ++
Sbjct: 496 VKLRAERDPEKVKAALDKITWAAGNPDDKDP--------DRNLLKLCIDAGRAMATVGEM 547
Query: 161 SRALRSVKGR 170
S AL V GR
Sbjct: 548 SDALEKVFGR 557
>pdb|3EIJ|A Chain A, Crystal Structure Of Pdcd4
pdb|3EIJ|B Chain B, Crystal Structure Of Pdcd4
Length = 321
Score = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 152 DQPELMSDLSRALRSVKGRLVRAEMVPVGGRIKCVLWVQGFKGNEGMVMLKRALN 206
D PEL D RA + V + RA VG I C ++ +KG V + AL+
Sbjct: 98 DLPELALDTPRAPQLVGQFIARA----VGDGILCNTYIDSYKGTVDCVQARAALD 148
>pdb|1E1C|A Chain A, Methylmalonyl-Coa Mutase H244a Mutant
pdb|1E1C|C Chain C, Methylmalonyl-Coa Mutase H244a Mutant
Length = 727
Score = 28.1 bits (61), Expect = 3.7, Method: Composition-based stats.
Identities = 32/130 (24%), Positives = 58/130 (44%), Gaps = 12/130 (9%)
Query: 45 ISKPISKVEAKELAAKKHSEAERRRRLRINDQYDNLRKILP-NLVKVDKASVLAKTIKTV 103
I K I K+ +E AA+ + + R+ I L P +++KVD ++VLA+ +
Sbjct: 436 IEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKL 495
Query: 104 RELQRTVREQK---ALCQVHEECVFPSEANELSLRNCNRDRGMLKVTLSCEDQPELMSDL 160
+L+ +K AL ++ P + + DR +LK+ + + ++
Sbjct: 496 VKLRAERDPEKVKAALDKITWAAGNPDDKDP--------DRNLLKLCIDAGRAMATVGEM 547
Query: 161 SRALRSVKGR 170
S AL V GR
Sbjct: 548 SDALEKVFGR 557
>pdb|3U5V|A Chain A, Crystal Structure Of Max-E47
Length = 76
Score = 27.7 bits (60), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 62 HSEAERRRRLRINDQYDNLRKILPNLVKVDKAS----VLAKTIKTVRELQRTVRE 112
H+ ER+RR IN+ + L ++ +K DKA +L + ++ + L++ VRE
Sbjct: 9 HNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRE 63
>pdb|2KZT|A Chain A, Structure Of The Tandem Ma-3 Region Of Pdcd4
Length = 163
Score = 27.3 bits (59), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 151 EDQPELMSDLSRALRSVKGRLVRAEMVPVGGRIKCVLWVQGFKGNEGMVMLKRALN 206
+D PEL D RA + V + RA VG I C ++ +KG V + AL+
Sbjct: 90 KDLPELALDTPRAPQLVGQFIARA----VGDGILCNTYIDSYKGTVDCVQARAALD 141
>pdb|2RG8|A Chain A, Crystal Structure Of Programmed For Cell Death 4 Middle
Ma3 Domain
pdb|2RG8|B Chain B, Crystal Structure Of Programmed For Cell Death 4 Middle
Ma3 Domain
Length = 165
Score = 27.3 bits (59), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 152 DQPELMSDLSRALRSVKGRLVRAEMVPVGGRIKCVLWVQGFKGNEGMVMLKRALN 206
D PEL D RA + V + RA VG I C ++ +KG V + AL+
Sbjct: 91 DLPELALDTPRAPQLVGQFIARA----VGDGILCNTYIDSYKGTVDCVQARAALD 141
>pdb|2F23|A Chain A, Crystal Structure Of Grea Factor Homolog 1 (Gfh1) Protein
Of Thermus Thermophilus
pdb|2F23|B Chain B, Crystal Structure Of Grea Factor Homolog 1 (Gfh1) Protein
Of Thermus Thermophilus
Length = 156
Score = 27.3 bits (59), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 64 EAERRRRLRINDQYDNLRKILPNLVKVDKASVLAKTIKTVRELQRTVREQKALCQVHEEC 123
EA ++ + RI + D+L IL V +++ S + +V EL+ + ++ QV
Sbjct: 49 EAAKQEKARIEARIDSLEDILSRAVILEEGSGEVIGLGSVVELEDPLSGERLSVQV---- 104
Query: 124 VFPSEANELS 133
V P+EAN L
Sbjct: 105 VSPAEANVLD 114
>pdb|2EUL|A Chain A, Structure Of The Transcription Factor Gfh1.
pdb|2EUL|B Chain B, Structure Of The Transcription Factor Gfh1.
pdb|2EUL|C Chain C, Structure Of The Transcription Factor Gfh1.
pdb|2EUL|D Chain D, Structure Of The Transcription Factor Gfh1.
pdb|3AOH|X Chain X, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|Y Chain Y, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|Z Chain Z, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOI|X Chain X, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|Y Chain Y, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|Z Chain Z, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
Length = 156
Score = 27.3 bits (59), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 64 EAERRRRLRINDQYDNLRKILPNLVKVDKASVLAKTIKTVRELQRTVREQKALCQVHEEC 123
EA ++ + RI + D+L IL V +++ S + +V EL+ + ++ QV
Sbjct: 49 EAAKQEKARIEARIDSLEDILSRAVILEEGSGEVIGLGSVVELEDPLSGERLSVQV---- 104
Query: 124 VFPSEANELS 133
V P+EAN L
Sbjct: 105 VSPAEANVLD 114
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
0.319 0.133 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,766,715
Number of Sequences: 62578
Number of extensions: 201825
Number of successful extensions: 530
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 523
Number of HSP's gapped (non-prelim): 27
length of query: 225
length of database: 14,973,337
effective HSP length: 95
effective length of query: 130
effective length of database: 9,028,427
effective search space: 1173695510
effective search space used: 1173695510
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)