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= psy842
(111 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3DMS|A Chain A, 1.65a Crystal Structure Of Isocitrate Dehydrogenase From
Burkholderia Pseudomallei
Length = 427
Score = 28.5 bits (62), Expect = 0.87, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 15 IAITADGTTVVCWHPEQPFPYEHSLPLPVTEQQSTNSILKVQNVQEIY 62
+A+ + VC P Q Y +P PV E + TN ++ +N ++IY
Sbjct: 126 VALRQELDLYVCLRPIQ---YFKGVPSPVREPEKTNMVIFRENSEDIY 170
>pdb|3LUA|A Chain A, Crystal Structure Of A Signal Receiver Domain Of Two
Component Signal Transduction (Histidine Kinase) From
Clostridium Thermocellum
Length = 140
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 13/76 (17%)
Query: 18 TADGTTVVCWHPEQPFPYEHSLPLPVTEQQSTNSILKVQNVQEIYNVFKPKKEEFVRQDL 77
+ DGT ++ + F YE + + ++V+N+++ Y++FK DL
Sbjct: 2 SLDGTVLLIDY----FEYEREKTKIIFDNIGEYDFIEVENLKKFYSIFK---------DL 48
Query: 78 MNITFTNKHRWFPVRK 93
+IT FPV K
Sbjct: 49 DSITLIIXDIAFPVEK 64
>pdb|2FTS|A Chain A, Crystal Structure Of The Glycine Receptor-Gephyrin Complex
pdb|2FU3|A Chain A, Crystal Structure Of Gephyrin E-Domain
pdb|2FU3|B Chain B, Crystal Structure Of Gephyrin E-Domain
Length = 419
Score = 25.8 bits (55), Expect = 6.0, Method: Composition-based stats.
Identities = 11/50 (22%), Positives = 27/50 (54%), Gaps = 6/50 (12%)
Query: 24 VVCWHPEQPFPYEHSLPLPVTEQQSTNSILKVQNVQEIYNVFKPKKEEFV 73
++ WH ++P P+ S T Q ++ ++ +++ + + PK E++V
Sbjct: 360 ILTWHHQEPLPWAQS-----TGNQMSSRLMSMRSANGLL-MLPPKTEQYV 403
>pdb|1T3E|A Chain A, Structural Basis Of Dynamic Glycine Receptor Clustering
pdb|1T3E|B Chain B, Structural Basis Of Dynamic Glycine Receptor Clustering
Length = 421
Score = 25.8 bits (55), Expect = 6.2, Method: Composition-based stats.
Identities = 11/50 (22%), Positives = 27/50 (54%), Gaps = 6/50 (12%)
Query: 24 VVCWHPEQPFPYEHSLPLPVTEQQSTNSILKVQNVQEIYNVFKPKKEEFV 73
++ WH ++P P+ S T Q ++ ++ +++ + + PK E++V
Sbjct: 362 ILTWHHQEPLPWAQS-----TGNQMSSRLMSMRSANGLL-MLPPKTEQYV 405
>pdb|3PPH|A Chain A, Crystal Structure Of The Candida Albicans Methionine
Synthase By Surface Entropy Reduction, Threonine Variant
pdb|3PPH|B Chain B, Crystal Structure Of The Candida Albicans Methionine
Synthase By Surface Entropy Reduction, Threonine Variant
Length = 789
Score = 25.8 bits (55), Expect = 6.9, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 43 VTEQQSTNSI-LKVQNVQEIYNVFKPKKEEFVRQDLMNITFTNKHRWFPVRKMRQKKRYF 101
V++Q N+ +K ++ I N PK +E R +N + FP R QK +Y
Sbjct: 404 VSKQLEANAASIKARSESSITN--DPKVQE--RLTTINEALATRKAAFPERLTEQKAKYN 459
Query: 102 KPLIP 106
PL P
Sbjct: 460 LPLFP 464
>pdb|3PPF|A Chain A, Crystal Structure Of The Candida Albicans Methionine
Synthase By Surface Entropy Reduction, Alanine Variant
Without Zinc
pdb|3PPG|A Chain A, Crystal Structure Of The Candida Albicans Methionine
Synthase By Surface Entropy Reduction, Alanine Variant
With Zinc
Length = 789
Score = 25.8 bits (55), Expect = 6.9, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 43 VTEQQSTNSI-LKVQNVQEIYNVFKPKKEEFVRQDLMNITFTNKHRWFPVRKMRQKKRYF 101
V++Q N+ +K ++ I N PK +E R +N + FP R QK +Y
Sbjct: 404 VSKQLEANAASIKARSESSITN--DPKVQE--RLTTINEALATRKAAFPERLTEQKAKYN 459
Query: 102 KPLIP 106
PL P
Sbjct: 460 LPLFP 464
>pdb|3PPC|A Chain A, Crystal Structure Of The Candida Albicans Methionine
Synthase By Surface Entropy Reduction, Tyrosine Variant
With Zinc
pdb|3PPC|B Chain B, Crystal Structure Of The Candida Albicans Methionine
Synthase By Surface Entropy Reduction, Tyrosine Variant
With Zinc
Length = 789
Score = 25.8 bits (55), Expect = 6.9, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 43 VTEQQSTNSI-LKVQNVQEIYNVFKPKKEEFVRQDLMNITFTNKHRWFPVRKMRQKKRYF 101
V++Q N+ +K ++ I N PK +E R +N + FP R QK +Y
Sbjct: 404 VSKQLEANAASIKARSESSITN--DPKVQE--RLTTINEALATRKAAFPERLTEQKAKYN 459
Query: 102 KPLIP 106
PL P
Sbjct: 460 LPLFP 464
>pdb|3Q73|A Chain A, Cryptococcus Neoformans Protein Farnesyltransferase, Apo
Enzyme
pdb|3Q75|A Chain A, Cryptococcus Neoformans Protein Farnesyltransferase In
Complex With Fpt-Ii And Tkcvvm Peptide
pdb|3Q78|A Chain A, Cryptococcus Neoformans Protein Farnesyltransferase In
Complex With Fspp And Ddptasacniq Peptide
pdb|3Q79|A Chain A, Cryptococcus Neoformans Protein Farnesyltransferase In
Complex With Farnesyl-Ddptasacniq Product
pdb|3Q7A|A Chain A, Cryptococcus Neoformans Protein Farnesyltransferase In
Complex With Fpp And L-778,123
pdb|3Q7F|A Chain A, Cryptococcus Neoformans Protein Farnesyltransferase In
Complex With Fpp And Ethylenediamine Inhibitor 1
Length = 349
Score = 25.4 bits (54), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 11/44 (25%), Positives = 21/44 (47%)
Query: 29 PEQPFPYEHSLPLPVTEQQSTNSILKVQNVQEIYNVFKPKKEEF 72
P P P + LP+P+ + +S ++ V + VF+ E+
Sbjct: 289 PSDPLPEDTPLPVPLALEYLADSFIEQNRVDDAAKVFEKLSSEY 332
>pdb|3SFX|A Chain A, Cryptococcus Neoformans Protein Farnesyltransferase In
Complex With Fpt-Ii And Tipifarnib
pdb|3SFY|A Chain A, Cryptococcus Neoformans Protein Farnesyltransferase In
Complex With Fpt-Ii And Ethylenediamine Inhibitor 2
Length = 349
Score = 25.4 bits (54), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 11/44 (25%), Positives = 21/44 (47%)
Query: 29 PEQPFPYEHSLPLPVTEQQSTNSILKVQNVQEIYNVFKPKKEEF 72
P P P + LP+P+ + +S ++ V + VF+ E+
Sbjct: 288 PSDPLPEDTPLPVPLALEYLADSFIEQNRVDDAAKVFEKLSSEY 331
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
0.322 0.136 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,324,382
Number of Sequences: 62578
Number of extensions: 121533
Number of successful extensions: 259
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 253
Number of HSP's gapped (non-prelim): 12
length of query: 111
length of database: 14,973,337
effective HSP length: 75
effective length of query: 36
effective length of database: 10,279,987
effective search space: 370079532
effective search space used: 370079532
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: 45 (21.9 bits)