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= psy13556
(127 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1U5M|A Chain A, Structure Of A Chordin-Like Cysteine-Rich Repeat (Vwc
Module) From Collagen Iia
Length = 73
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 62 CEHNGKVYNNGEKLNSTLTPCQVCYCRGGALMCTHFTCFTRDDCQGRTLP-GTCCP 116
C +G+ YN+ + PC++C C G ++C C DC +P G CCP
Sbjct: 10 CVQDGQRYNDKDVWKPE--PCRICVCDTGTVLCDDIICEDVKDCLSPEIPFGECCP 63
Score = 25.8 bits (55), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 21 PCEECRCTDGTVVCSMMQCEIKPGCQTIQRP-NQCCP 56
PC C C GTV+C + CE C + + P +CCP
Sbjct: 27 PCRICVCDTGTVLCDDIICEDVKDCLSPEIPFGECCP 63
>pdb|2P3J|A Chain A, Crystal Structure Of The Arg101ala Mutant Protein Of
Rhesus Rotavirus Vp8
Length = 161
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 27/68 (39%), Gaps = 12/68 (17%)
Query: 19 FGPCEECRCTDGTVVCSMMQCEIKPGCQTIQR-------PNQCCPEFKCECEHNGKVYN- 70
FG E+ + S Q + +T Q P Q P+ +HNGK+Y
Sbjct: 59 FGTQEQITIAN----ASQTQWKFIDVVKTTQNGSYSQYGPLQSTPKLYAVMKHNGKIYTY 114
Query: 71 NGEKLNST 78
NGE N T
Sbjct: 115 NGETPNVT 122
>pdb|2P3I|A Chain A, Crystal Structure Of Rhesus Rotavirus Vp8 At 295k
pdb|2P3K|A Chain A, Crystal Structure Of Rhesus Rotavirus Vp8* At 100k
pdb|3TB0|A Chain A, Crystal Structure Of Rhesus Rotavirus Vp8 In Complex With
N- Glycolylneuraminic Acid
Length = 161
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 27/68 (39%), Gaps = 12/68 (17%)
Query: 19 FGPCEECRCTDGTVVCSMMQCEIKPGCQTIQR-------PNQCCPEFKCECEHNGKVYN- 70
FG E+ + S Q + +T Q P Q P+ +HNGK+Y
Sbjct: 59 FGTQEQITIAN----ASQTQWKFIDVVKTTQNGSYSQYGPLQSTPKLYAVMKHNGKIYTY 114
Query: 71 NGEKLNST 78
NGE N T
Sbjct: 115 NGETPNVT 122
>pdb|1KRI|A Chain A, Nmr Solution Structures Of The Rhesus Rotavirus Vp4 Sialic
Acid Binding Domain Without Ligand
Length = 186
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 27/68 (39%), Gaps = 12/68 (17%)
Query: 19 FGPCEECRCTDGTVVCSMMQCEIKPGCQTIQR-------PNQCCPEFKCECEHNGKVYN- 70
FG E+ + S Q + +T Q P Q P+ +HNGK+Y
Sbjct: 77 FGTQEQITIAN----ASQTQWKFIDVVKTTQNGSYSQYGPLQSTPKLYAVMKHNGKIYTY 132
Query: 71 NGEKLNST 78
NGE N T
Sbjct: 133 NGETPNVT 140
>pdb|1KQR|A Chain A, Crystal Structure Of The Rhesus Rotavirus Vp4 Sialic Acid
Binding Domain In Complex With
2-o-methyl-alpha-d-n-acetyl Neuraminic Acid
Length = 179
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 27/68 (39%), Gaps = 12/68 (17%)
Query: 19 FGPCEECRCTDGTVVCSMMQCEIKPGCQTIQR-------PNQCCPEFKCECEHNGKVYN- 70
FG E+ + S Q + +T Q P Q P+ +HNGK+Y
Sbjct: 77 FGTQEQITIAN----ASQTQWKFIDVVKTTQNGSYSQYGPLQSTPKLYAVMKHNGKIYTY 132
Query: 71 NGEKLNST 78
NGE N T
Sbjct: 133 NGETPNVT 140
>pdb|4H2H|A Chain A, Crystal Structure Of An Enolase (Mandalate Racemase
Subgroup, Target Efi-502101) From Pelagibaca Bermudensis
Htcc2601, With Bound Mg And L-4-Hydroxyproline Betaine
(Betonicine)
pdb|4H2H|B Chain B, Crystal Structure Of An Enolase (Mandalate Racemase
Subgroup, Target Efi-502101) From Pelagibaca Bermudensis
Htcc2601, With Bound Mg And L-4-Hydroxyproline Betaine
(Betonicine)
pdb|4H2H|C Chain C, Crystal Structure Of An Enolase (Mandalate Racemase
Subgroup, Target Efi-502101) From Pelagibaca Bermudensis
Htcc2601, With Bound Mg And L-4-Hydroxyproline Betaine
(Betonicine)
pdb|4H2H|D Chain D, Crystal Structure Of An Enolase (Mandalate Racemase
Subgroup, Target Efi-502101) From Pelagibaca Bermudensis
Htcc2601, With Bound Mg And L-4-Hydroxyproline Betaine
(Betonicine)
pdb|4H2H|E Chain E, Crystal Structure Of An Enolase (Mandalate Racemase
Subgroup, Target Efi-502101) From Pelagibaca Bermudensis
Htcc2601, With Bound Mg And L-4-Hydroxyproline Betaine
(Betonicine)
pdb|4H2H|F Chain F, Crystal Structure Of An Enolase (Mandalate Racemase
Subgroup, Target Efi-502101) From Pelagibaca Bermudensis
Htcc2601, With Bound Mg And L-4-Hydroxyproline Betaine
(Betonicine)
pdb|4H2H|G Chain G, Crystal Structure Of An Enolase (Mandalate Racemase
Subgroup, Target Efi-502101) From Pelagibaca Bermudensis
Htcc2601, With Bound Mg And L-4-Hydroxyproline Betaine
(Betonicine)
pdb|4H2H|H Chain H, Crystal Structure Of An Enolase (Mandalate Racemase
Subgroup, Target Efi-502101) From Pelagibaca Bermudensis
Htcc2601, With Bound Mg And L-4-Hydroxyproline Betaine
(Betonicine)
Length = 376
Score = 27.7 bits (60), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 23/59 (38%), Gaps = 7/59 (11%)
Query: 62 CEHNGKVYNNGEKLNSTLTPCQVCYCRGGALMCT------HFTCFTRDDCQGRTLPGTC 114
C H + +G LN+ +T G + + H F RD C R LP TC
Sbjct: 243 CHHALYMDEDGTSLNTVITAAATSLVDGFGMKVSRIGGLQHMRAF-RDFCAARNLPHTC 300
>pdb|3IYU|X Chain X, Atomic Model Of An Infectious Rotavirus Particle
pdb|3IYU|Y Chain Y, Atomic Model Of An Infectious Rotavirus Particle
pdb|3IYU|Z Chain Z, Atomic Model Of An Infectious Rotavirus Particle
Length = 776
Score = 26.9 bits (58), Expect = 2.9, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 51 PNQCCPEFKCECEHNGKVYN-NGEKLNST 78
P Q P+ +HNGK+Y NGE N T
Sbjct: 157 PLQSTPKLYAVMKHNGKIYTYNGETPNVT 185
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
0.326 0.143 0.528
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,419,921
Number of Sequences: 62578
Number of extensions: 171185
Number of successful extensions: 538
Number of sequences better than 100.0: 36
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 502
Number of HSP's gapped (non-prelim): 60
length of query: 127
length of database: 14,973,337
effective HSP length: 87
effective length of query: 40
effective length of database: 9,529,051
effective search space: 381162040
effective search space used: 381162040
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)