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= psy4017
(136 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2GVS|A Chain A, Nmr Solution Structure Of Cspsg4
Length = 109
Score = 130 bits (327), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 60/100 (60%), Positives = 81/100 (81%), Gaps = 2/100 (2%)
Query: 25 EKYTTKYDNVDLDQILKNDRLFNNYYNCLL--DKGKCSPDGQELKNKLPDAIATECKSCS 82
EKYTTKYDNV+LD+IL NDRL N Y CLL D+ C+ DG+ELK+ +PDA++ EC C+
Sbjct: 2 EKYTTKYDNVNLDEILANDRLLNKYVQCLLEDDESNCTADGKELKSVIPDALSNECAKCN 61
Query: 83 EKQKEGSKKIFKYLIDNKPEQWAELEKKFDPNGTYKAKYQ 122
EKQKEG+KK+ K+LI++KP+ WA+L+ K+DP+GTY KY+
Sbjct: 62 EKQKEGTKKVLKHLINHKPDVWAQLKAKYDPDGTYSKKYE 101
>pdb|1KX8|A Chain A, Antennal Chemosensory Protein A6 From Mamestra Brassicae,
Tetragonal Form
pdb|1KX9|A Chain A, Antennal Chemosensory Protein A6 From The Moth Mamestra
Brassicae
pdb|1KX9|B Chain B, Antennal Chemosensory Protein A6 From The Moth Mamestra
Brassicae
pdb|1N8U|A Chain A, Chemosensory Protein In Complex With Bromo-Dodecanol
pdb|1N8V|A Chain A, Chemosensory Protein In Complex With Bromo-Dodecanol
pdb|1N8V|B Chain B, Chemosensory Protein In Complex With Bromo-Dodecanol
pdb|1K19|A Chain A, Nmr Solution Structure Of The Chemosensory Protein Csp2
From Moth Mamestra Brassicae
Length = 112
Score = 113 bits (282), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 49/98 (50%), Positives = 72/98 (73%)
Query: 25 EKYTTKYDNVDLDQILKNDRLFNNYYNCLLDKGKCSPDGQELKNKLPDAIATECKSCSEK 84
+KYT KYDN++LD+IL N RL Y NC++++GKCSP+G+ELK L DAI CK C+E
Sbjct: 2 DKYTDKYDNINLDEILANKRLLVAYVNCVMERGKCSPEGKELKEHLQDAIENGCKKCTEN 61
Query: 85 QKEGSKKIFKYLIDNKPEQWAELEKKFDPNGTYKAKYQ 122
Q++G+ ++ ++LI N+ E W EL K+DP G ++ KY+
Sbjct: 62 QEKGAYRVIEHLIKNEIEIWRELTAKYDPTGNWRKKYE 99
>pdb|2JNT|A Chain A, Structure Of Bombyx Mori Chemosensory Protein 1 In
Solution
Length = 108
Score = 102 bits (255), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 45/96 (46%), Positives = 69/96 (71%)
Query: 27 YTTKYDNVDLDQILKNDRLFNNYYNCLLDKGKCSPDGQELKNKLPDAIATECKSCSEKQK 86
YT KYD ++L +IL+N RL +Y +C+L KGKC+P+G+ELK+ L +A+ T C+ C+E Q+
Sbjct: 1 YTDKYDKINLQEILENKRLLESYMDCVLGKGKCTPEGKELKDHLQEALETGCEKCTEAQE 60
Query: 87 EGSKKIFKYLIDNKPEQWAELEKKFDPNGTYKAKYQ 122
+G++ YLI N+ E W EL FDP+G ++ KY+
Sbjct: 61 KGAETSIDYLIKNELEIWKELTAHFDPDGKWRKKYE 96
>pdb|3PSI|A Chain A, Crystal Structure Of The Spt6 Core Domain From
Saccharomyces Cerevisiae, Form Spt6(239-1451)
Length = 1219
Score = 29.6 bits (65), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 54 LDKGKCSPDGQELKNKLP-DAIATECKSCSEKQKEGSKKIFKYLIDNKPEQWAELE 108
LD + P+ L K+ DA+ + + +EK+++G+ F L+ P++ A+LE
Sbjct: 784 LDSTRIHPEDYHLATKVAADALEYDPDTIAEKEEQGTMSEFIELLREDPDRRAKLE 839
>pdb|3PSF|A Chain A, Crystal Structure Of The Spt6 Core Domain From
Saccharomyces Cerevisiae, Form Spt6(236-1259)
Length = 1030
Score = 29.3 bits (64), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 54 LDKGKCSPDGQELKNKLP-DAIATECKSCSEKQKEGSKKIFKYLIDNKPEQWAELE 108
LD + P+ L K+ DA+ + + +EK+++G+ F L+ P++ A+LE
Sbjct: 787 LDSTRIHPEDYHLATKVAADALEYDPDTIAEKEEQGTMSEFIELLREDPDRRAKLE 842
>pdb|2VN8|A Chain A, Crystal Structure Of Human Reticulon 4 Interacting Protein
1 In Complex With Nadph
pdb|2VN8|B Chain B, Crystal Structure Of Human Reticulon 4 Interacting Protein
1 In Complex With Nadph
Length = 375
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 59 CSPDGQELKNKLPDAIATECKSCSEKQKEGSKKIFKYLIDN---KPEQWA 105
CS D EL KL + KS S +++ S K F +++DN E WA
Sbjct: 215 CSQDASELVRKLGADDVIDYKSGSVEEQLKSLKPFDFILDNVGGSTETWA 264
>pdb|1U3C|A Chain A, Crystal Structure Of The Phr Domain Of Cryptochrome 1 From
Arabidopsis Thaliana
pdb|1U3D|A Chain A, Crystal Structure Of The Phr Domain Of Cryptochrome 1 From
Arabidopsis Thaliana With Amppnp Bound
Length = 509
Score = 26.9 bits (58), Expect = 3.7, Method: Composition-based stats.
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 110 KFDPNGTYKAKYQKELSDL 128
KFDPNG Y ++ ELS L
Sbjct: 425 KFDPNGEYVRRWLPELSRL 443
>pdb|3CVX|A Chain A, Drosophila Melanogaster (6-4) Photolyase H369m Mutant
Bound To Ds Dna With A T-T (6-4) Photolesion
Length = 543
Score = 26.9 bits (58), Expect = 3.9, Method: Composition-based stats.
Identities = 13/23 (56%), Positives = 13/23 (56%)
Query: 109 KKFDPNGTYKAKYQKELSDLKAG 131
KK DP G Y KY ELS AG
Sbjct: 453 KKTDPQGHYIRKYVPELSKYPAG 475
>pdb|3CVU|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Ds Dna
With A T-T (6-4) Photolesion
pdb|3CVY|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Repaired
Ds Dna
pdb|2WB2|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Double
Stranded Dna Containing A T(6-4)c Photolesion
pdb|3CVV|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Ds Dna
With A T-T (6-4) Photolesion And F0 Cofactor
pdb|2WQ6|A Chain A, Structure Of The 6-4 Photolyase Of D. Melanogaster In
Complex With The Non-Natural N4-Methyl T(Dewar)c Lesion
pdb|2WQ7|A Chain A, Structure Of The 6-4 Photolyase Of D. Melanogaster In
Complex With The Non-Natural N4-Methyl T(6-4)c Lesion
Length = 543
Score = 26.9 bits (58), Expect = 3.9, Method: Composition-based stats.
Identities = 13/23 (56%), Positives = 13/23 (56%)
Query: 109 KKFDPNGTYKAKYQKELSDLKAG 131
KK DP G Y KY ELS AG
Sbjct: 453 KKTDPQGHYIRKYVPELSKYPAG 475
>pdb|3CVW|A Chain A, Drosophila Melanogaster (6-4) Photolyase H365n Mutant
Bound To Ds Dna With A T-T (6-4) Photolesion And
Cofactor F0
Length = 543
Score = 26.6 bits (57), Expect = 4.0, Method: Composition-based stats.
Identities = 13/23 (56%), Positives = 13/23 (56%)
Query: 109 KKFDPNGTYKAKYQKELSDLKAG 131
KK DP G Y KY ELS AG
Sbjct: 453 KKTDPQGHYIRKYVPELSKYPAG 475
>pdb|4AM9|A Chain A, Crystal Structure Of The Yersinia Enterocolitica Type Iii
Secretion Chaperone Sycd In Complex With A Peptide Of
The Translocator Yopd
Length = 148
Score = 26.6 bits (57), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 3 KLCSAAVGLFLAVQLVAGKPAGEKYTTKYDNV 34
+L A GLFLA +L+A KP ++ +T+ ++
Sbjct: 104 ELAEAESGLFLAQELIANKPEFKELSTRVSSM 135
>pdb|1XM9|A Chain A, Structure Of The Armadillo Repeat Domain Of Plakophilin 1
Length = 457
Score = 25.4 bits (54), Expect = 9.2, Method: Composition-based stats.
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 41 KNDRLFNNYYNCLLDKGKCSPDG 63
K+D++ NN Y+C L + + +P G
Sbjct: 253 KSDKMMNNNYDCPLPEEETNPKG 275
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 0.134 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,679,953
Number of Sequences: 62578
Number of extensions: 205114
Number of successful extensions: 482
Number of sequences better than 100.0: 41
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 459
Number of HSP's gapped (non-prelim): 41
length of query: 136
length of database: 14,973,337
effective HSP length: 88
effective length of query: 48
effective length of database: 9,466,473
effective search space: 454390704
effective search space used: 454390704
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: 46 (22.3 bits)