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= 038298
(259 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/113 (23%), Positives = 57/113 (50%), Gaps = 12/113 (10%)
Query: 97 QEHVIAERKRREKMNQQFIALSAVIPGI----KQMNKASVLEGTIKHLKELQERGKKLVE 152
+ H E++RR+KMN L++++P ++++K +VL ++H+K L+ E
Sbjct: 15 EAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYTE 74
Query: 153 HTKRKAPESVVSVKRSQQTLPDIVVRVSDNNVLIRIHCEKQNIGFISNIVSEI 205
+ P + S L +++R +D + + + C++ I F+S V +I
Sbjct: 75 ANYK--PTFL-----SDDELKHLILRAADGFLFV-VGCDRGKILFVSESVFKI 119
>pdb|2A1X|A Chain A, Human Phytanoyl-Coa 2-Hydroxylase In Complex With Iron And
2- Oxoglutarate
Length = 308
Score = 34.7 bits (78), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 3/52 (5%)
Query: 56 YCTIKSEDKRA---SDENLMAMKTRIVNKPGQGNRVASRSPLQAQEHVIAER 104
YCT+ K + N+MAM T ++NKP + SR PL H R
Sbjct: 103 YCTLPEILKYVECFTGPNIMAMHTMLINKPPDSGKKTSRHPLHQDLHYFPFR 154
>pdb|1GAX|A Chain A, Crystal Structure Of Thermus Thermophilus Valyl-Trna
Synthetase Complexed With Trna(Val) And Valyl-Adenylate
Analogue
pdb|1GAX|B Chain B, Crystal Structure Of Thermus Thermophilus Valyl-Trna
Synthetase Complexed With Trna(Val) And Valyl-Adenylate
Analogue
pdb|1IVS|A Chain A, Crystal Structure Of Thermus Thermophilus Valyl-Trna
Synthetase Complexed With Trna(Val) And Valyl-Adenylate
Analogue
pdb|1IVS|B Chain B, Crystal Structure Of Thermus Thermophilus Valyl-Trna
Synthetase Complexed With Trna(Val) And Valyl-Adenylate
Analogue
pdb|1IYW|A Chain A, Preliminary Structure Of Thermus Thermophilus Ligand-Free
Valyl-Trna Synthetase
pdb|1IYW|B Chain B, Preliminary Structure Of Thermus Thermophilus Ligand-Free
Valyl-Trna Synthetase
Length = 862
Score = 33.5 bits (75), Expect = 0.11, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 87 RVASRSPLQAQEHVIAERKRREKMNQQFIALSA------VIPGIKQMNKASVLEGTIKHL 140
RV +R PL+ V R+R+EK ++ +AL+ PG ++ V+E L
Sbjct: 785 RVTARMPLEGLLDVEEWRRRQEKRLKELLALAERSQRKLASPGFREKAPKEVVEAEEARL 844
Query: 141 KELQERGKKLVE 152
KE E+ +++ E
Sbjct: 845 KENLEQAERIRE 856
>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 361
Score = 32.3 bits (72), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 32/45 (71%), Gaps = 1/45 (2%)
Query: 102 AERKRREKMNQQFIALSAVIPG-IKQMNKASVLEGTIKHLKELQE 145
+E+KRR++ N L +++PG ++M+K++VL+ +I L++ +E
Sbjct: 19 SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKE 63
>pdb|3HMC|A Chain A, Endolysin From Bacillus Anthracis
Length = 192
Score = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 7/57 (12%)
Query: 176 VVRVSDNNVLIRIHCEKQNIGFI-------SNIVSEIEKLHLVVINSRTIPFGNYAL 225
++ +S N I KQ+I FI SN V + K ++ + IPFGNYA
Sbjct: 7 IIDISKWNGDINWSIAKQHIDFIIARVQDGSNYVDPLYKGYVQAMKQHGIPFGNYAF 63
>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 = 31.2 bits (69), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 32/45 (71%), Gaps = 1/45 (2%)
Query: 102 AERKRREKMNQQFIALSAVIPG-IKQMNKASVLEGTIKHLKELQE 145
+E+KRR++ N L +++PG ++M+K++VL+ +I L++ +E
Sbjct: 15 SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKE 59
>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 = 31.2 bits (69), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 32/52 (61%), Gaps = 4/52 (7%)
Query: 97 QEHVIAERKRREKMNQQFIALSAVIPGI----KQMNKASVLEGTIKHLKELQ 144
+ H E++RR+KMN L++++P ++++K +VL ++H+K L+
Sbjct: 11 EAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 62
>pdb|2NW0|A Chain A, Crystal Structure Of A Lysin
pdb|2NW0|B Chain B, Crystal Structure Of A Lysin
Length = 189
Score = 30.4 bits (67), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 199 SNIVSEIEKLHLVVINSRTIPFGNYAL 225
SN V + K ++ + +R IPFG+YA
Sbjct: 33 SNYVDPVYKDYVAAMKARNIPFGSYAF 59
>pdb|3BCV|A Chain A, Crystal Structure Of A Putative Glycosyltransferase From
Bacteroides Fragilis
pdb|3BCV|B Chain B, Crystal Structure Of A Putative Glycosyltransferase From
Bacteroides Fragilis
Length = 240
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 30/113 (26%), Positives = 50/113 (44%), Gaps = 19/113 (16%)
Query: 119 AVIPGIKQMNKASVLEGTIKHLKELQERGKKLVEHTKRKAPESVVSVKRSQQTLPDIVVR 178
AV G+K++ A + GT+ H KE + K HT K + R ++ ++
Sbjct: 116 AVFTGLKRITXAGIPTGTVTHQKEFKLYKNKNEIHTLLKDLIASDPYAREERA-----IQ 170
Query: 179 VSDNNVLIRIHCEKQNIGFISNIVSEIEKLHLVVINSRTIPFGNYALDITVVA 231
VS VL R +N+ IEK HL ++ R +P + ++ V+A
Sbjct: 171 VSAKVVLYR-----RNL---------IEKKHLRFVSERILPSEDLIFNVDVLA 209
>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 = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 13/71 (18%)
Query: 99 HVIAERKRREKMNQQFIALSAVIPGIK----QMNKASVLEGTIKHLKEL---QERGKKL- 150
H + ER+RR +N + L +IP + NK ++L+ ++ ++++L Q+R K L
Sbjct: 31 HNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLE 90
Query: 151 -----VEHTKR 156
+EH R
Sbjct: 91 NRQKKLEHANR 101
>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 = 28.9 bits (63), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 98 EHVIAERKRREKMNQQFIALSAVIP 122
+H ER+RR+K+N + LS +IP
Sbjct: 8 QHNEVERRRRDKINNWIVQLSKIIP 32
>pdb|2B5D|X Chain X, Crystal Structure Of The Novel Alpha-Amylase Amyc From
Thermotoga Maritima
Length = 528
Score = 28.1 bits (61), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 25/104 (24%), Positives = 44/104 (42%), Gaps = 16/104 (15%)
Query: 98 EHVIAERKRREKMNQQFIAL--------------SAVIPGIKQMNKASVLEGTIKHLKEL 143
+H + ER E + + +I L S P ++ ++ + E +H+++L
Sbjct: 22 DHFLEERWLFEAITETYIPLLMMFDEIEDFRLTMSITPPLMEMLSSRDLQEKYERHMEKL 81
Query: 144 QERGKKLVEHTKRKAPESVVSVKRSQQTLPDI--VVRVSDNNVL 185
E K VE TK++ P K ++ I V R D N+L
Sbjct: 82 IELANKEVERTKKEHPLKHKMAKFYREHFEKILNVFRSYDGNIL 125
>pdb|2Z7J|A Chain A, Structural Insights Into De Multifunctional Vp3 Protein
Of Birnaviruses:gold Derivative
Length = 125
Score = 28.1 bits (61), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 47 QMSNPNSEYYCTIKSEDKR-ASDENLMAMKTRIVNKPGQ 84
++ +PN +Y + +E R AS+E ++ T I PGQ
Sbjct: 47 EIPDPNEDYLDYVHAEKSRLASEEQILRAATSIYGAPGQ 85
>pdb|2R18|A Chain A, Structural Insights Into The Multifunctional Protein Vp3
Of Birnaviruses
Length = 139
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 47 QMSNPNSEYYCTIKSEDKR-ASDENLMAMKTRIVNKPGQ 84
++ +PN +Y + +E R AS+E ++ T I PGQ
Sbjct: 60 EIPDPNEDYLDYVHAEKSRLASEEQILRAATSIYGAPGQ 98
>pdb|3NTL|A Chain A, Crystal Structure Of Glucose-1-Phosphatase (Agpe) From
Enterobacter Cloacae
pdb|3NTL|B Chain B, Crystal Structure Of Glucose-1-Phosphatase (Agpe) From
Enterobacter Cloacae
Length = 398
Score = 27.3 bits (59), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 68 DENLMAMKTRIVNKPGQGNRVASRSPLQAQEHVIAERKRREKMNQQFIALSAVIPGIKQM 127
D N+ ++ T + KP Q + R+P+ + ++ +R + NQ+ + + V +Q+
Sbjct: 288 DSNIASLLTALDFKPYQLHDQQERTPIGGK--IVFQRWHDKNANQELMKIEYVYQSSEQL 345
Query: 128 NKASVL 133
ASVL
Sbjct: 346 RNASVL 351
>pdb|2PH3|A Chain A, Crystal Structure Of 3-oxoacyl-[acyl Carrier Protein]
Reductase Ttha0415 From Thermus Thermophilus
pdb|2PH3|B Chain B, Crystal Structure Of 3-oxoacyl-[acyl Carrier Protein]
Reductase Ttha0415 From Thermus Thermophilus
Length = 245
Score = 27.3 bits (59), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 5/47 (10%)
Query: 78 IVNKPGQGNRVASRSPLQAQEHVIAERKRREKMNQQFIALSAVIPGI 124
I+ PGQ N VAS++ L +A ++ Q+ I ++AV PG
Sbjct: 143 ILGNPGQANYVASKAGLIGFTRAVA-----KEYAQRGITVNAVAPGF 184
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 0.130 0.352
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,499,073
Number of Sequences: 62578
Number of extensions: 231833
Number of successful extensions: 737
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 733
Number of HSP's gapped (non-prelim): 21
length of query: 259
length of database: 14,973,337
effective HSP length: 97
effective length of query: 162
effective length of database: 8,903,271
effective search space: 1442329902
effective search space used: 1442329902
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: 50 (23.9 bits)