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= psy4958
(65 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2GEE|A Chain A, Crystal Structure Of Human Type Iii Fibronectin
Extradomain B And Domain 8
Length = 203
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 29/55 (52%), Gaps = 6/55 (10%)
Query: 7 GRAYNISVQTVSEDEISTPTTAQYRTI--PLRPLSFTYDKASITSNSLRVVWEPP 59
G Y+ISV TV STPTT +T P L FT +I +++RV W PP
Sbjct: 87 GIDYDISVYTVKNGGESTPTTLTQQTAVPPPTDLRFT----NIGPDTMRVTWAPP 137
>pdb|1FNF|A Chain A, Fragment Of Human Fibronectin Encompassing Type-Iii
Repeats 7 Through 10
Length = 368
Score = 30.8 bits (68), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 7 GRAYNISVQTVSEDEISTPTTAQYRTIPLRPLSFTYDKASITSNSLRVVWEPP 59
G YN+SV TV +D+ S P + IP P +I +++RV W PP
Sbjct: 68 GLEYNVSVYTVKDDKESVPISDTI--IPAVPPPTDLRFTNIGPDTMRVTWAPP 118
Score = 27.3 bits (59), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 7 GRAYNISVQTVSEDEISTPTTAQYRTIPLRPLSFTYDKASITSNSLRVVWEPPKG 61
G Y +SV +V E STP + +T P D + IT+NS V W P+
Sbjct: 159 GTEYVVSVSSVYEQHESTPLRGRQKTGLDSPTGI--DFSDITANSFTVHWIAPRA 211
>pdb|2VBI|A Chain A, Holostructure Of Pyruvate Decarboxylase From Acetobacter
Pasteurianus
pdb|2VBI|B Chain B, Holostructure Of Pyruvate Decarboxylase From Acetobacter
Pasteurianus
pdb|2VBI|C Chain C, Holostructure Of Pyruvate Decarboxylase From Acetobacter
Pasteurianus
pdb|2VBI|D Chain D, Holostructure Of Pyruvate Decarboxylase From Acetobacter
Pasteurianus
pdb|2VBI|E Chain E, Holostructure Of Pyruvate Decarboxylase From Acetobacter
Pasteurianus
pdb|2VBI|F Chain F, Holostructure Of Pyruvate Decarboxylase From Acetobacter
Pasteurianus
pdb|2VBI|G Chain G, Holostructure Of Pyruvate Decarboxylase From Acetobacter
Pasteurianus
pdb|2VBI|H Chain H, Holostructure Of Pyruvate Decarboxylase From Acetobacter
Pasteurianus
Length = 566
Score = 28.9 bits (63), Expect = 0.81, Method: Composition-based stats.
Identities = 15/51 (29%), Positives = 29/51 (56%), Gaps = 5/51 (9%)
Query: 7 GRAYN-----ISVQTVSEDEISTPTTAQYRTIPLRPLSFTYDKASITSNSL 52
GRAY+ +Q ++E + P +AQ ++P L+ T D+A +T++ +
Sbjct: 316 GRAYDGFTLRAFLQALAEKAPARPASAQKSSVPTCSLTATSDEAGLTNDEI 366
>pdb|1QR4|A Chain A, Two Fibronectin Type-Iii Domain Segment From Chicken
Tenascin
pdb|1QR4|B Chain B, Two Fibronectin Type-Iii Domain Segment From Chicken
Tenascin
Length = 186
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 4 IGTGRAYNISVQTVSEDEISTPTTAQYRTIPLRPLSFTYDKASITSNSLRVVWEPPK 60
+ G Y IS+ S PTT + T+ P ++ + IT NS V W PP+
Sbjct: 65 LDAGTEYTISLVAEKGRHKSKPTTIKGSTVVGSPKGISF--SDITENSATVSWTPPR 119
>pdb|3T1W|A Chain A, Structure Of The Four-Domain Fragment Fn7b89 Of Oncofetal
Fibronectin
Length = 375
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 7 GRAYNISVQTVSEDEISTPTTAQYRTIPLRPLSFTYDKASITSNSLRVVWEPPKG 61
G Y +SV +V E STP + +T P D + IT+NS V W P+
Sbjct: 251 GTEYVVSVSSVYEQHESTPLRGRQKTGLDSPTGI--DFSDITANSFTVHWIAPRA 303
Score = 26.2 bits (56), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 7 GRAYNISVQTVSEDEISTPTTAQYRTIPLRPLSFTYDKASITSNSLRVVWEP 58
G YN+SV TV +D+ S P + IP P IT +S+ + W P
Sbjct: 69 GLEYNVSVYTVKDDKESVPISDTI--IPEVPQLTDLSFVDITDSSIGLRWTP 118
>pdb|4GH7|B Chain B, Crystal Structure Of Anticalin N7a In Complex With
Oncofetal Fibronectin Fragment Fn7b8
pdb|4GH7|D Chain D, Crystal Structure Of Anticalin N7a In Complex With
Oncofetal Fibronectin Fragment Fn7b8
Length = 285
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 7 GRAYNISVQTVSEDEISTPTTAQYRTIPLRPLSFTYDKASITSNSLRVVWEP 58
G YN+SV TV +D+ S P + IP P IT +S+ + W P
Sbjct: 69 GLEYNVSVYTVKDDKESVPISDTI--IPEVPQLTDLSFVDITDSSIGLRWTP 118
>pdb|2CRM|A Chain A, Solution Structure Of The Forth Fniii Domain Of Human
Length = 120
Score = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 17/28 (60%), Gaps = 4/28 (14%)
Query: 33 IPLRPLSFTYDKASITSNSLRVVWEPPK 60
IP++P K I S+S ++ W+PPK
Sbjct: 20 IPVKPSV----KGKIHSHSFKITWDPPK 43
>pdb|3B9K|L Chain L, Crystal Structure Of Cd8alpha-Beta In Complex With Yts
156.7 Fab
pdb|3B9K|C Chain C, Crystal Structure Of Cd8alpha-Beta In Complex With Yts
156.7 Fab
Length = 213
Score = 25.4 bits (54), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 5 GTGRAYNISVQTVSEDEISTPTTAQYRTI 33
G+GR Y S+ +V ++I++ QY T+
Sbjct: 66 GSGRDYTFSISSVESEDIASYYCLQYDTL 94
>pdb|3IY1|A Chain A, Variable Domains Of The Wam Of Fab B Fitted Into The
Cryoem Reconstruction Of The Virus-Fab B Complex
Length = 107
Score = 25.4 bits (54), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 5 GTGRAYNISVQTVSEDEISTPTTAQYRTIP 34
G+GR Y+ S+ V ++I++ QY + P
Sbjct: 64 GSGRDYSFSISNVESEDIASYYCLQYDSSP 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
0.316 0.132 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,932,390
Number of Sequences: 62578
Number of extensions: 56350
Number of successful extensions: 269
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 259
Number of HSP's gapped (non-prelim): 20
length of query: 65
length of database: 14,973,337
effective HSP length: 36
effective length of query: 29
effective length of database: 12,720,529
effective search space: 368895341
effective search space used: 368895341
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)