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= psy13975
(415 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3Q3J|B Chain B, Crystal Structure Of Plexin A2 Rbd In Complex With Rnd1
Length = 214
Score = 35.0 bits (79), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 22/110 (20%), Positives = 41/110 (37%), Gaps = 4/110 (3%)
Query: 21 NILLISDNSSGKTTLIAKLQGIDSPEKGLALEYAYINVSDEYREDHTRLGVWILDGEPAH 80
++L+ D GKT ++ L PE + + E E L +W G P +
Sbjct: 29 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYY 88
Query: 81 SNLLRFALNQETLPHTMVMLVVSMTTPWNIIDELHNWASVLQDHIDSLNI 130
N+ + V+L ++ P + L W + + D+ S +
Sbjct: 89 DNVRPLCYSD----SDAVLLCFDISRPETVDSALKKWRTEILDYCPSTRV 134
>pdb|2REX|B Chain B, Crystal Structure Of The Effector Domain Of Plxnb1 Bound
With Rnd1 Gtpase
pdb|2REX|D Chain D, Crystal Structure Of The Effector Domain Of Plxnb1 Bound
With Rnd1 Gtpase
Length = 197
Score = 34.7 bits (78), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 22/110 (20%), Positives = 41/110 (37%), Gaps = 4/110 (3%)
Query: 21 NILLISDNSSGKTTLIAKLQGIDSPEKGLALEYAYINVSDEYREDHTRLGVWILDGEPAH 80
++L+ D GKT ++ L PE + + E E L +W G P +
Sbjct: 12 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYY 71
Query: 81 SNLLRFALNQETLPHTMVMLVVSMTTPWNIIDELHNWASVLQDHIDSLNI 130
N+ + V+L ++ P + L W + + D+ S +
Sbjct: 72 DNVRPLCYSD----SDAVLLCFDISRPETVDSALKKWRTEILDYCPSTRV 117
>pdb|2CLS|A Chain A, The Crystal Structure Of The Human Rnd1 Gtpase In The
Active Gtp Bound State
pdb|2CLS|B Chain B, The Crystal Structure Of The Human Rnd1 Gtpase In The
Active Gtp Bound State
Length = 198
Score = 34.7 bits (78), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 22/110 (20%), Positives = 41/110 (37%), Gaps = 4/110 (3%)
Query: 21 NILLISDNSSGKTTLIAKLQGIDSPEKGLALEYAYINVSDEYREDHTRLGVWILDGEPAH 80
++L+ D GKT ++ L PE + + E E L +W G P +
Sbjct: 13 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYY 72
Query: 81 SNLLRFALNQETLPHTMVMLVVSMTTPWNIIDELHNWASVLQDHIDSLNI 130
N+ + V+L ++ P + L W + + D+ S +
Sbjct: 73 DNVRPLCYSD----SDAVLLCFDISRPETVDSALKKWRTEILDYCPSTRV 118
>pdb|1FAO|A Chain A, Structure Of The Pleckstrin Homology Domain From
Dapp1PHISH IN COMPLEX WITH INOSITOL 1,3,4,5-
Tetrakisphosphate
pdb|1FB8|A Chain A, Structure Of The Pleckstrin Homology Domain From
Dapp1/phish
Length = 126
Score = 28.9 bits (63), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 19/42 (45%)
Query: 206 HFDFVQQYIRKFCLKFGAGLFYTSAKEDKNCDLLYKYLAHRL 247
FD+ Q+ + FCL F FY AK D K L +L
Sbjct: 70 QFDYSQERVNCFCLVFPFRTFYLCAKTGVEADEWIKILRWKL 111
>pdb|3J16|B Chain B, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
Length = 608
Score = 28.9 bits (63), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 9 FVLRFNDGSVIGN--ILLISDNSSGKTTLIAKLQGIDSPEKG 48
FVL +G + ++++ +N +GKTTLI L G P++G
Sbjct: 366 FVLNVEEGEFSDSEILVMMGENGTGKTTLIKLLAGALKPDEG 407
>pdb|1YQT|A Chain A, Rnase-L Inhibitor
Length = 538
Score = 28.5 bits (62), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 16 GSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
G VIG ++ N GKTT + L G++ P +G
Sbjct: 312 GEVIG---IVGPNGIGKTTFVKXLAGVEEPTEG 341
>pdb|3J15|B Chain B, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 593
Score = 28.5 bits (62), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 16 GSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
G VIG ++ N GKTT + L G++ P +G
Sbjct: 368 GEVIG---IVGPNGIGKTTFVKMLAGVEEPTEG 397
>pdb|1GWN|A Chain A, The Crystal Structure Of The Core Domain Of RhoeRND3 - A
Constitutively Activated Small G Protein
pdb|1GWN|C Chain C, The Crystal Structure Of The Core Domain Of RhoeRND3 - A
Constitutively Activated Small G Protein
Length = 205
Score = 28.5 bits (62), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 21/107 (19%), Positives = 40/107 (37%), Gaps = 4/107 (3%)
Query: 17 SVIGNILLISDNSSGKTTLIAKLQGIDSPEKGLALEYAYINVSDEYREDHTRLGVWILDG 76
+V I+++ D+ GKT L+ PE + + S E L +W G
Sbjct: 26 NVKCKIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYTASFEIDTQRIELSLWDTSG 85
Query: 77 EPAHSNLLRFALNQETLPHTMVMLVVSMTTPWNIIDELHNWASVLQD 123
P + N+ + V++ ++ P + L W +Q+
Sbjct: 86 SPYYDNVRPLSYPDS----DAVLICFDISRPETLDSVLKKWKGEIQE 128
>pdb|3BK7|A Chain A, Structure Of The Complete Abce1RNAASE-L Inhibitor Protein
From Pyrococcus Abysii
Length = 607
Score = 28.5 bits (62), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 16 GSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
G VIG ++ N GKTT + L G++ P +G
Sbjct: 382 GEVIG---IVGPNGIGKTTFVKMLAGVEEPTEG 411
>pdb|1Z47|A Chain A, Structure Of The Atpase Subunit Cysa Of The Putative
Sulfate Atp-Binding Cassette (Abc) Transporter From
Alicyclobacillus Acidocaldarius
pdb|1Z47|B Chain B, Structure Of The Atpase Subunit Cysa Of The Putative
Sulfate Atp-Binding Cassette (Abc) Transporter From
Alicyclobacillus Acidocaldarius
Length = 355
Score = 28.1 bits (61), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
+ +G ++G L+ + SGKTT++ + G++ P KG
Sbjct: 36 FQIREGEMVG---LLGPSGSGKTTILRLIAGLERPTKG 70
>pdb|2V55|B Chain B, Mechanism Of Multi-site Phosphorylation From A Rock-i:rhoe
Complex Structure
pdb|2V55|D Chain D, Mechanism Of Multi-site Phosphorylation From A Rock-i:rhoe
Complex Structure
Length = 200
Score = 28.1 bits (61), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 22/108 (20%), Positives = 42/108 (38%), Gaps = 6/108 (5%)
Query: 17 SVIGNILLISDNSSGKTTLIAKLQGIDSPEKGLALEYAYINVSDEYREDHTRLGVWILDG 76
+V I+++ D+ GKT L+ PE + + S E L +W G
Sbjct: 21 NVKCKIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYTASFEIDTQRIELSLWDTSG 80
Query: 77 EPAHSNLLRFALNQETLPHT-MVMLVVSMTTPWNIIDELHNWASVLQD 123
P + N+ + P + V++ ++ P + L W +Q+
Sbjct: 81 SPYYDNVRPL-----SYPDSDAVLICFDISRPETLDSVLKKWKGEIQE 123
>pdb|1M7B|A Chain A, Crystal Structure Of Rnd3RHOE: FUNCTIONAL IMPLICATIONS
Length = 184
Score = 28.1 bits (61), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 21/107 (19%), Positives = 40/107 (37%), Gaps = 4/107 (3%)
Query: 17 SVIGNILLISDNSSGKTTLIAKLQGIDSPEKGLALEYAYINVSDEYREDHTRLGVWILDG 76
+V I+++ D+ GKT L+ PE + + S E L +W G
Sbjct: 5 NVKCKIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYTASFEIDTQRIELSLWDTSG 64
Query: 77 EPAHSNLLRFALNQETLPHTMVMLVVSMTTPWNIIDELHNWASVLQD 123
P + N+ + V++ ++ P + L W +Q+
Sbjct: 65 SPYYDNVRPLSYPDS----DAVLICFDISRPETLDSVLKKWKGEIQE 107
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 0.136 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,474,649
Number of Sequences: 62578
Number of extensions: 524358
Number of successful extensions: 1263
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1255
Number of HSP's gapped (non-prelim): 21
length of query: 415
length of database: 14,973,337
effective HSP length: 101
effective length of query: 314
effective length of database: 8,652,959
effective search space: 2717029126
effective search space used: 2717029126
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)