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= psy6009
(866 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CNW|D Chain D, Gdpalf4 Complex Of The Srp Gtpases Ffh And Ftsy
pdb|2CNW|E Chain E, Gdpalf4 Complex Of The Srp Gtpases Ffh And Ftsy
pdb|2CNW|F Chain F, Gdpalf4 Complex Of The Srp Gtpases Ffh And Ftsy
pdb|2IYL|D Chain D, Structure Of An Ftsy:gdp Complex
Length = 284
Score = 31.2 bits (69), Expect = 2.5, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 649 KMNALNEVNKVIAGVAYYPHRHPEEEWLTPDRQLTESGLKCFEKFFKSVNI 699
K N + E+ KV +A P+E WL D ++GL+ +KF ++V +
Sbjct: 179 KHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQAKKFHEAVGL 229
>pdb|2J7P|D Chain D, Gmppnp-Stabilized Ng Domain Complex Of The Srp Gtpases Ffh
And Ftsy
pdb|2J7P|E Chain E, Gmppnp-Stabilized Ng Domain Complex Of The Srp Gtpases Ffh
And Ftsy
Length = 283
Score = 31.2 bits (69), Expect = 2.5, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 649 KMNALNEVNKVIAGVAYYPHRHPEEEWLTPDRQLTESGLKCFEKFFKSVNI 699
K N + E+ KV +A P+E WL D ++GL+ +KF ++V +
Sbjct: 178 KHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQAKKFHEAVGL 228
>pdb|1XYK|A Chain A, Nmr Structure Of The Canine Prion Protein
Length = 111
Score = 30.4 bits (67), Expect = 4.9, Method: Composition-based stats.
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 173 DEIFARPIDYYKNQRGWLVDLINL 196
D+++ RP+D Y NQ ++ D +N+
Sbjct: 39 DQVYYRPVDQYSNQNNFVRDCVNI 62
>pdb|1RJ9|A Chain A, Structure Of The Heterodimer Of The Conserved Gtpase
Domains Signal Recognition Particle (Ffh) And Its
Receptor (Ftsy)
Length = 304
Score = 30.0 bits (66), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 649 KMNALNEVNKVIAGVAYYPHRHPEEEWLTPDRQLTESGLKCFEKFFKSVNI 699
K N + E+ KV +A P+E WL D ++GL+ +KF ++V +
Sbjct: 199 KHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQAKKFHEAVGL 249
>pdb|1OKK|D Chain D, Homo-Heterodimeric Complex Of The Srp Gtpases
pdb|2XKV|D Chain D, Atomic Model Of The Srp-Ftsy Early Conformation
Length = 303
Score = 30.0 bits (66), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 649 KMNALNEVNKVIAGVAYYPHRHPEEEWLTPDRQLTESGLKCFEKFFKSVNI 699
K N + E+ KV +A P+E WL D ++GL+ +KF ++V +
Sbjct: 198 KHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQAKKFHEAVGL 248
>pdb|2Q9A|A Chain A, Structure Of Apo Ftsy
pdb|2Q9A|B Chain B, Structure Of Apo Ftsy
pdb|2Q9B|A Chain A, Structure Of Ftsy:gmppnp Complex
pdb|2Q9B|B Chain B, Structure Of Ftsy:gmppnp Complex
pdb|2Q9C|A Chain A, Structure Of Ftsy:gmppnp With Mgcl Complex
pdb|2Q9C|B Chain B, Structure Of Ftsy:gmppnp With Mgcl Complex
Length = 304
Score = 30.0 bits (66), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 649 KMNALNEVNKVIAGVAYYPHRHPEEEWLTPDRQLTESGLKCFEKFFKSVNI 699
K N + E+ KV +A P+E WL D ++GL+ +KF ++V +
Sbjct: 199 KHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQAKKFHEAVGL 249
>pdb|1KWG|A Chain A, Crystal Structure Of Thermus Thermophilus A4
Beta-Galactosidase
pdb|1KWK|A Chain A, Crystal Structure Of Thermus Thermophilus A4
Beta-Galactosidase In Complex With Galactose
Length = 645
Score = 30.0 bits (66), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 20/40 (50%), Gaps = 7/40 (17%)
Query: 662 GVAYYPHRHPEEEWLTPDRQLTESGLKCFEKFFKSVNIGE 701
GV YYP P+E W R++ E+GL V IGE
Sbjct: 3 GVCYYPEHWPKERWKEDARRMREAGL-------SHVRIGE 35
>pdb|2OIF|A Chain A, The Crystal Structure Of Ferric Cyanide Bound Barley
Hexacoordinate Hemoglobin.
pdb|2OIF|B Chain B, The Crystal Structure Of Ferric Cyanide Bound Barley
Hexacoordinate Hemoglobin.
pdb|2OIF|C Chain C, The Crystal Structure Of Ferric Cyanide Bound Barley
Hexacoordinate Hemoglobin.
pdb|2OIF|D Chain D, The Crystal Structure Of Ferric Cyanide Bound Barley
Hexacoordinate Hemoglobin.
pdb|2OIF|E Chain E, The Crystal Structure Of Ferric Cyanide Bound Barley
Hexacoordinate Hemoglobin.
pdb|2OIF|F Chain F, The Crystal Structure Of Ferric Cyanide Bound Barley
Hexacoordinate Hemoglobin.
pdb|2OIF|G Chain G, The Crystal Structure Of Ferric Cyanide Bound Barley
Hexacoordinate Hemoglobin.
pdb|2OIF|H Chain H, The Crystal Structure Of Ferric Cyanide Bound Barley
Hexacoordinate Hemoglobin
Length = 162
Score = 29.6 bits (65), Expect = 6.7, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 241 LKYFMPILEIVP---EILENLTDEELKKEAKNESKNDAISVIIKSCKLLA 287
L++F+ I EI P ++ L D ++ E + K A+SV + +C+ A
Sbjct: 34 LRFFLKIFEIAPSARQMFPFLRDSDVPLETNPKLKTHAVSVFVMTCEAAA 83
>pdb|2LH8|A Chain A, Syrian Hamster Prion Protein With Thiamine
Length = 104
Score = 29.6 bits (65), Expect = 7.8, Method: Composition-based stats.
Identities = 10/30 (33%), Positives = 19/30 (63%)
Query: 167 NSNIADDEIFARPIDYYKNQRGWLVDLINL 196
N N ++++ RP+D Y NQ ++ D +N+
Sbjct: 29 NMNRYPNQVYYRPVDQYNNQNNFVHDCVNI 58
>pdb|2K56|A Chain A, Bank Vole Prion Protein (121-231)
Length = 113
Score = 29.6 bits (65), Expect = 7.8, Method: Composition-based stats.
Identities = 10/30 (33%), Positives = 19/30 (63%)
Query: 167 NSNIADDEIFARPIDYYKNQRGWLVDLINL 196
N N ++++ RP+D Y NQ ++ D +N+
Sbjct: 35 NMNRYPNQVYYRPVDQYNNQNNFVHDCVNI 64
>pdb|1B10|A Chain A, Solution Nmr Structure Of Recombinant Syrian Hamster Prion
Protein Rprp(90-231) , 25 Structures
Length = 142
Score = 29.6 bits (65), Expect = 8.1, Method: Composition-based stats.
Identities = 10/30 (33%), Positives = 19/30 (63%)
Query: 167 NSNIADDEIFARPIDYYKNQRGWLVDLINL 196
N N ++++ RP+D Y NQ ++ D +N+
Sbjct: 64 NMNRYPNQVYYRPVDQYNNQNNFVHDCVNI 93
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 0.137 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,327,301
Number of Sequences: 62578
Number of extensions: 1028274
Number of successful extensions: 2456
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 2440
Number of HSP's gapped (non-prelim): 24
length of query: 866
length of database: 14,973,337
effective HSP length: 107
effective length of query: 759
effective length of database: 8,277,491
effective search space: 6282615669
effective search space used: 6282615669
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)