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= 016128
(394 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4EA3|A Chain A, Structure Of The NOFQ OPIOID RECEPTOR IN COMPLEX WITH A
PEPTIDE Mimetic
pdb|4EA3|B Chain B, Structure Of The NOFQ OPIOID RECEPTOR IN COMPLEX WITH A
PEPTIDE Mimetic
Length = 434
Score = 33.5 bits (75), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 5/68 (7%)
Query: 234 SAVEIFDLMQQEKVKPNSASFVAVLSACGHAGHVDKALQ--IFTMMDDDFGLKPKQEHFG 291
+ V++F L Q V+P+S + VA+L C G+V+ L ++ +D++F K F
Sbjct: 351 TPVQVFVLAQGLGVQPSSETAVAILRFCTALGYVNSCLNPILYAFLDENF--KACFRKF- 407
Query: 292 CMVDLLGR 299
C LGR
Sbjct: 408 CCASALGR 415
>pdb|1ZT2|A Chain A, Heterodimeric Structure Of The Core Primase.
pdb|1ZT2|C Chain C, Heterodimeric Structure Of The Core Primase
Length = 330
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 6/65 (9%)
Query: 245 EKVKPNSASFVAVLSACGHAGHVDKALQIFTMMDDDFGLKPK-----QEHFGCMVDLLGR 299
E+ + +V + S C G +++ + +++DDFGLKPK F VD G
Sbjct: 129 ERDNVETLEYVEMTSECIKRG-LEQTRNLVEILEDDFGLKPKVYFSGNRGFHVQVDCYGN 187
Query: 300 SGRLD 304
LD
Sbjct: 188 CALLD 192
>pdb|3KD7|A Chain A, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
pdb|3KD7|B Chain B, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
pdb|3KD7|C Chain C, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
pdb|3KD7|D Chain D, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
pdb|3KD7|E Chain E, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
Length = 125
Score = 30.4 bits (67), Expect = 2.0, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 193 YMKCGQPSWARRFFDQ-FEIKPDDPAFWNAMISGYGRNGEYESAVEIFDLMQQEKVKPNS 251
Y K G A ++ + E+ P++ + W + + Y + G+Y+ A+E + + ++ PN+
Sbjct: 19 YYKQGDYQKAIEYYQKALELDPNNASAWYNLGNAYYKQGDYQKAIEYYQ--KALELDPNN 76
Query: 252 A 252
A
Sbjct: 77 A 77
Score = 29.6 bits (65), Expect = 3.3, Method: Composition-based stats.
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 179 LNKDESMATA---LISMYMKCGQPSWARRFFDQ-FEIKPDDPAFWNAMISGYGRNGEYES 234
L D + A+A L + Y K G A ++ + E+ P++ W + Y + G+Y+
Sbjct: 36 LELDPNNASAWYNLGNAYYKQGDYQKAIEYYQKALELDPNNAKAWYRRGNAYYKQGDYQK 95
Query: 235 AVEIFDLMQQEKVKPNSA 252
A+E D + ++ PN+A
Sbjct: 96 AIE--DYQKALELDPNNA 111
>pdb|1NA0|A Chain A, Design Of Stable Alpha-Helical Arrays From An Idealized
Tpr Motif
pdb|1NA0|B Chain B, Design Of Stable Alpha-Helical Arrays From An Idealized
Tpr Motif
Length = 125
Score = 30.0 bits (66), Expect = 2.3, Method: Composition-based stats.
Identities = 19/84 (22%), Positives = 44/84 (52%), Gaps = 4/84 (4%)
Query: 193 YMKCGQPSWARRFFDQ-FEIKPDDPAFWNAMISGYGRNGEYESAVEIFDLMQQEKVKPNS 251
Y K G A ++ + E+ P++ W + + Y + G+Y+ A+E + + ++ PN+
Sbjct: 19 YYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQ--KALELDPNN 76
Query: 252 A-SFVAVLSACGHAGHVDKALQIF 274
A ++ + +A G D+A++ +
Sbjct: 77 AEAWYNLGNAYYKQGDYDEAIEYY 100
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 218 FWNAMISGYGRNGEYESAVEIFDLMQQEKVKPNSASFVAVLSACGH----AGHVDKALQ 272
+NA++ G+ R G ++ V + +++ + P+ S+ A L G AG +++ L+
Sbjct: 167 MYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLE 225
>pdb|1NA3|A Chain A, Design Of Stable Alpha-Helical Arrays From An Idealized
Tpr Motif
pdb|1NA3|B Chain B, Design Of Stable Alpha-Helical Arrays From An Idealized
Tpr Motif
Length = 91
Score = 29.3 bits (64), Expect = 3.9, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 193 YMKCGQPSWARRFFDQ-FEIKPDDPAFWNAMISGYGRNGEYESAVEIFDLMQQEKVKPNS 251
Y K G A ++ + E+ P++ W + + Y + G+Y+ A+E + + ++ PN+
Sbjct: 19 YYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQ--KALELDPNN 76
Query: 252 A 252
A
Sbjct: 77 A 77
>pdb|2WQH|A Chain A, Crystal Structure Of Ctpr3y3
Length = 125
Score = 29.3 bits (64), Expect = 4.5, Method: Composition-based stats.
Identities = 19/84 (22%), Positives = 44/84 (52%), Gaps = 4/84 (4%)
Query: 193 YMKCGQPSWARRFFDQ-FEIKPDDPAFWNAMISGYGRNGEYESAVEIFDLMQQEKVKPNS 251
Y K G A ++ + E+ P++ W + + Y + G+Y+ A+E + + ++ PN+
Sbjct: 19 YYKQGDYDEAIEYYQKALELYPNNAEAWYNLGNAYYKQGDYDEAIEYYQ--KALELYPNN 76
Query: 252 A-SFVAVLSACGHAGHVDKALQIF 274
A ++ + +A G D+A++ +
Sbjct: 77 AEAWYNLGNAYYKQGDYDEAIEYY 100
>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Ca
Length = 501
Score = 28.9 bits (63), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 1/73 (1%)
Query: 237 EIFDLMQQEKVKPNSASFVAVLSACGHAGHVDKALQIFTMMDDDFGLKPKQEHFGCMVDL 296
+IF M +KV PN A+F + A + M FG++P+ +G +
Sbjct: 91 DIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKA-FGIQPRLRSYGPALFG 149
Query: 297 LGRSGRLDEAREL 309
R G D+A E+
Sbjct: 150 FCRKGDADKAYEV 162
>pdb|2DLL|A Chain A, Solution Structure Of The Irf Domain Of Human Interferon
Regulator Factors 4
Length = 121
Score = 28.5 bits (62), Expect = 7.0, Method: Composition-based stats.
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 96 KAMELFEGLAHEGF-KPDPATWNSMI 120
KA LF+G EG KPDP TW + +
Sbjct: 57 KAWALFKGKFREGIDKPDPPTWKTRL 82
>pdb|3G8Q|A Chain A, A Cytidine Deaminase Edits C-To-U In Transfer Rnas In
Archaea
pdb|3G8Q|B Chain B, A Cytidine Deaminase Edits C-To-U In Transfer Rnas In
Archaea
pdb|3G8Q|C Chain C, A Cytidine Deaminase Edits C-To-U In Transfer Rnas In
Archaea
pdb|3G8Q|D Chain D, A Cytidine Deaminase Edits C-To-U In Transfer Rnas In
Archaea
Length = 278
Score = 28.1 bits (61), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 35/147 (23%), Positives = 63/147 (42%), Gaps = 16/147 (10%)
Query: 225 GYGRN-GEY---ESAVEIFDLMQQEKVKPNSASFVAVLSACGHAGHV---DKALQIFTMM 277
G GR G Y S VE+ ++ E + + + VL G ++ D A +++ ++
Sbjct: 86 GRGRGLGPYYLARSGVEVVEVHPDEPLGYDPVDRLDVLLTFGGNPYLTEEDVAARVYCLL 145
Query: 278 DD---DFGLKPKQEHFGCMVDLLGRSGRLDEARELIRELPEPTVSVYHSLLGACWCHLNS 334
D + P E+ V+++ G DEA EL++E P + L+ +
Sbjct: 146 TGRGFDADIAPAPENLSGRVEIMVTRGDPDEAVELLKE-ELPVFRIRRFLISGEF----- 199
Query: 335 DLGEEMAMKLQEMEPENPTPFVILSNI 361
D E L+++EP PF + + I
Sbjct: 200 DRDELRERILEDIEPRILDPFAVRARI 226
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
0.321 0.135 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,587,816
Number of Sequences: 62578
Number of extensions: 461859
Number of successful extensions: 998
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 984
Number of HSP's gapped (non-prelim): 21
length of query: 394
length of database: 14,973,337
effective HSP length: 101
effective length of query: 293
effective length of database: 8,652,959
effective search space: 2535316987
effective search space used: 2535316987
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)