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= 046200
(212 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3A2E|A Chain A, Crystal Structure Of Ginkbilobin-2, The Novel Antifungal
Protein From Ginkgo Biloba Seeds
pdb|3A2E|B Chain B, Crystal Structure Of Ginkbilobin-2, The Novel Antifungal
Protein From Ginkgo Biloba Seeds
pdb|3A2E|C Chain C, Crystal Structure Of Ginkbilobin-2, The Novel Antifungal
Protein From Ginkgo Biloba Seeds
pdb|3A2E|D Chain D, Crystal Structure Of Ginkbilobin-2, The Novel Antifungal
Protein From Ginkgo Biloba Seeds
Length = 108
Score = 30.4 bits (67), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 28/67 (41%), Gaps = 1/67 (1%)
Query: 51 YLYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCIKVAIHTIVTNCTGAKEAIVWYDQCMV 110
Y S A G P YG C+ +S C C+ ++ I + C A A V C +
Sbjct: 43 YKTSRAGSGGAP-TAYGRATCKQSISQSDCTACLSNLVNRIFSICNNAIGARVQLVDCFI 101
Query: 111 RFCNSSF 117
++ SF
Sbjct: 102 QYEQRSF 108
>pdb|3QWU|A Chain A, Putative Atp-Dependent Dna Ligase From Aquifex Aeolicus.
pdb|3QWU|B Chain B, Putative Atp-Dependent Dna Ligase From Aquifex Aeolicus
Length = 370
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 32/81 (39%), Gaps = 7/81 (8%)
Query: 31 LFMFNVGTLFSAKLYNEAGRY----LYSNATEGDYPDKVYGLYNCRFDVSND---VCQDC 83
LFM+ G + LY E GR L+ + + KVY + C+F + + +
Sbjct: 264 LFMYEEGLKTTEHLYEELGRAFIDGLFQAIEQFEKEHKVYKTFTCKFRKKENAIALLELL 323
Query: 84 IKVAIHTIVTNCTGAKEAIVW 104
K + H V KE W
Sbjct: 324 SKTSKHIQVKERRLEKEGDYW 344
>pdb|1XYK|A Chain A, Nmr Structure Of The Canine Prion Protein
Length = 111
Score = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 4/73 (5%)
Query: 29 GGLFMFNVGTLFSAKLYNEAGRY--LYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCIKV 86
GGL + +G+ S L + Y Y YPD+VY ++ N+ +DC+ +
Sbjct: 3 GGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPDQVYYRPVDQYSNQNNFVRDCVNI 62
Query: 87 AI--HTIVTNCTG 97
+ HT+ T G
Sbjct: 63 TVKQHTVTTTTKG 75
>pdb|1Y2S|A Chain A, Ovine Prion Protein Variant R168
Length = 113
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 4/73 (5%)
Query: 29 GGLFMFNVGTLFSAKLYNEAGRY--LYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCIKV 86
GGL + +G+ S L + Y Y YP++VY R+ N+ DC+ +
Sbjct: 5 GGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDRYSNQNNFVHDCVNI 64
Query: 87 AI--HTIVTNCTG 97
+ HT+ T G
Sbjct: 65 TVKQHTVTTTTKG 77
>pdb|2K56|A Chain A, Bank Vole Prion Protein (121-231)
Length = 113
Score = 28.5 bits (62), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 8/75 (10%)
Query: 29 GGLFMFNVGTLFSAKLYNEAG----RYLYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCI 84
GGL + +G+ S + + RY N YP++VY +++ N+ DC+
Sbjct: 5 GGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMNR--YPNQVYYRPVDQYNNQNNFVHDCV 62
Query: 85 KVAI--HTIVTNCTG 97
+ I HT+ T G
Sbjct: 63 NITIKQHTVTTTTKG 77
>pdb|2KU5|A Chain A, Mouse Prion Protein (121-231) With Mutation D167s
Length = 113
Score = 28.5 bits (62), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 29 GGLFMFNVGTLFSAKLYNEAG----RYLYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCI 84
GGL + +G+ S + + RY N YP++VY ++ N+ DC+
Sbjct: 4 GGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYR--YPNQVYYRPVSQYSNQNNFVHDCV 61
Query: 85 KVAI--HTIVTNCTG 97
+ I HT+ T G
Sbjct: 62 NITIKQHTVTTTTKG 76
>pdb|1DWY|A Chain A, Bovine Prion Protein Fragment 121-230
pdb|1DWZ|A Chain A, Bovine Prion Protein Fragment 121-230
Length = 112
Score = 27.7 bits (60), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 4/73 (5%)
Query: 29 GGLFMFNVGTLFSAKLYNEAGRY--LYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCIKV 86
GGL + +G+ S L + Y Y YP++VY ++ N+ DC+ +
Sbjct: 5 GGLGGYMLGSAMSRPLIHFGSDYEDRYYRENMHRYPNQVYYRPVDQYSNQNNFVHDCVNI 64
Query: 87 AI--HTIVTNCTG 97
+ HT+ T G
Sbjct: 65 TVKEHTVTTTTKG 77
>pdb|4DGI|A Chain A, Structure Of Pom1 Fab Fragment Complexed With Human Prpc
Fragment 120- 230
Length = 111
Score = 27.7 bits (60), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 4/73 (5%)
Query: 29 GGLFMFNVGTLFSAKLYNEAGRY--LYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCIKV 86
GGL + +G+ S + + Y Y YP++VY + N+ DC+ +
Sbjct: 4 GGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNI 63
Query: 87 AI--HTIVTNCTG 97
I HT+ T G
Sbjct: 64 TIKQHTVTTTTKG 76
>pdb|2KFO|A Chain A, Mouse Prion Protein (121-231) With Mutation V166a
Length = 114
Score = 27.7 bits (60), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 29 GGLFMFNVGTLFSAKLYNEAG----RYLYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCI 84
GGL + +G+ S + + RY N YP++VY ++ N+ DC+
Sbjct: 5 GGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYR--YPNQVYYRPADQYSNQNNFVHDCV 62
Query: 85 KVAI--HTIVTNCTG 97
+ I HT+ T G
Sbjct: 63 NITIKQHTVTTTTKG 77
>pdb|2K5O|A Chain A, Mouse Prion Protein (121-231) With Mutation S170n
Length = 114
Score = 27.7 bits (60), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 8/75 (10%)
Query: 29 GGLFMFNVGTLFSAKLYNEAG----RYLYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCI 84
GGL + +G+ S + + RY N YP++VY +++ N+ DC+
Sbjct: 5 GGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYR--YPNQVYYRPVDQYNNQNNFVHDCV 62
Query: 85 KVAI--HTIVTNCTG 97
+ I HT+ T G
Sbjct: 63 NITIKQHTVTTTTKG 77
>pdb|2W9E|A Chain A, Structure Of Icsm 18 (Anti-Prp Therapeutic Antibody) Fab
Fragment Complexed With Human Prp Fragment 119-231
Length = 113
Score = 27.7 bits (60), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 4/73 (5%)
Query: 29 GGLFMFNVGTLFSAKLYNEAGRY--LYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCIKV 86
GGL + +G+ S + + Y Y YP++VY + N+ DC+ +
Sbjct: 5 GGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNI 64
Query: 87 AI--HTIVTNCTG 97
I HT+ T G
Sbjct: 65 TIKQHTVTTTTKG 77
>pdb|1QM2|A Chain A, Human Prion Protein Fragment 121-230
pdb|1QM3|A Chain A, Human Prion Protein Fragment 121-230
Length = 112
Score = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 4/73 (5%)
Query: 29 GGLFMFNVGTLFSAKLYNEAGRY--LYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCIKV 86
GGL + +G+ S + + Y Y YP++VY + N+ DC+ +
Sbjct: 5 GGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNI 64
Query: 87 AI--HTIVTNCTG 97
I HT+ T G
Sbjct: 65 TIKQHTVTTTTKG 77
>pdb|1I4M|A Chain A, Crystal Structure Of The Human Prion Protein Reveals A
Mechanism For Oligomerization
Length = 108
Score = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 4/73 (5%)
Query: 29 GGLFMFNVGTLFSAKLYNEAGRY--LYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCIKV 86
GGL + +G+ S + + Y Y YP++VY + N+ DC+ +
Sbjct: 5 GGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNI 64
Query: 87 AI--HTIVTNCTG 97
I HT+ T G
Sbjct: 65 TIKQHTVTTTTKG 77
>pdb|2L1E|A Chain A, Mouse Prion Protein (121-231) Containing The
Substitution F175a
Length = 114
Score = 27.3 bits (59), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 29 GGLFMFNVGTLFSAKLYNEAG----RYLYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCI 84
GGL + +G+ S + + RY N YP++VY ++ N+ DC+
Sbjct: 5 GGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYR--YPNQVYYRPVDQYSNQNNAVHDCV 62
Query: 85 KVAI--HTIVTNCTG 97
+ I HT+ T G
Sbjct: 63 NITIKQHTVTTTTKG 77
>pdb|1XYJ|A Chain A, Nmr Structure Of The Cat Prion Protein
Length = 111
Score = 27.3 bits (59), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 4/73 (5%)
Query: 29 GGLFMFNVGTLFSAKLYNEAGRY--LYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCIKV 86
GGL + +G+ S L + Y Y YP++VY ++ N+ DC+ +
Sbjct: 3 GGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDQYSNQNNFVHDCVNI 62
Query: 87 AI--HTIVTNCTG 97
+ HT+ T G
Sbjct: 63 TVRQHTVTTTTKG 75
>pdb|2KFM|A Chain A, Mouse Prion Protein (121-231) With Mutations Y225a And
Y226a
Length = 114
Score = 27.3 bits (59), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 29 GGLFMFNVGTLFSAKLYNEAG----RYLYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCI 84
GGL + +G+ S + + RY N YP++VY ++ N+ DC+
Sbjct: 5 GGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYR--YPNQVYYRPVDQYSNQNNFVHDCV 62
Query: 85 KVAI--HTIVTNCTG 97
+ I HT+ T G
Sbjct: 63 NITIKQHTVTTTTKG 77
>pdb|1B10|A Chain A, Solution Nmr Structure Of Recombinant Syrian Hamster Prion
Protein Rprp(90-231) , 25 Structures
Length = 142
Score = 27.3 bits (59), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 50 RYLYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCIKVAI--HTIVTNCTGA 98
RY N YP++VY +++ N+ DC+ + I HT+ T G
Sbjct: 59 RYYRENMNR--YPNQVYYRPVDQYNNQNNFVHDCVNITIKQHTVTTTTKGE 107
>pdb|1XYX|A Chain A, Mouse Prion Protein Fragment 121-231
Length = 112
Score = 27.3 bits (59), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 29 GGLFMFNVGTLFSAKLYNEAG----RYLYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCI 84
GGL + +G+ S + + RY N YP++VY ++ N+ DC+
Sbjct: 3 GGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYR--YPNQVYYRPVDQYSNQNNFVHDCV 60
Query: 85 KVAI--HTIVTNCTG 97
+ I HT+ T G
Sbjct: 61 NITIKQHTVTTTTKG 75
>pdb|2L1H|A Chain A, Mouse Prion Protein Fragment 121-231 At 20 C
pdb|2L39|A Chain A, Mouse Prion Protein Fragment 121-231 At 37 C
Length = 114
Score = 27.3 bits (59), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 29 GGLFMFNVGTLFSAKLYNEAG----RYLYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCI 84
GGL + +G+ S + + RY N YP++VY ++ N+ DC+
Sbjct: 5 GGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYR--YPNQVYYRPVDQYSNQNNFVHDCV 62
Query: 85 KVAI--HTIVTNCTG 97
+ I HT+ T G
Sbjct: 63 NITIKQHTVTTTTKG 77
>pdb|1TQC|A Chain A, Ovine Recombinant Prp(114-234), Arr Variant In Complex
With The Vrq14 Fab Fragment (Igg2a)
Length = 102
Score = 26.9 bits (58), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 61 YPDKVYGLYNCRFDVSNDVCQDCIKVAI--HTIVTNCTG 97
YP++VY R+ N+ DC+ + + HT+ T G
Sbjct: 34 YPNQVYYRPVDRYSNQNNFVHDCVNITVKQHTVTTTTKG 72
>pdb|1XYU|A Chain A, Solution Structure Of The Sheep Prion Protein With
Polymorphism H168
Length = 111
Score = 26.9 bits (58), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 4/73 (5%)
Query: 29 GGLFMFNVGTLFSAKLYNEAGRY--LYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCIKV 86
GGL + +G+ S L + Y Y YP++VY + N+ DC+ +
Sbjct: 3 GGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDHYSNQNNFVHDCVNI 62
Query: 87 AI--HTIVTNCTG 97
+ HT+ T G
Sbjct: 63 TVKQHTVTTTTKG 75
>pdb|1XYW|A Chain A, Elk Prion Protein
Length = 111
Score = 26.9 bits (58), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 4/73 (5%)
Query: 29 GGLFMFNVGTLFSAKLYNEAGRY--LYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCIKV 86
GGL + +G+ S L + Y Y YP++VY +++ N DC+ +
Sbjct: 3 GGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDQYNNQNTFVHDCVNI 62
Query: 87 AI--HTIVTNCTG 97
+ HT+ T G
Sbjct: 63 TVKQHTVTTTTKG 75
>pdb|1Y16|A Chain A, Mouse Prion Protein With Mutations S170n And N174t
Length = 112
Score = 26.9 bits (58), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 29 GGLFMFNVGTLFSAKLYNEAG----RYLYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCI 84
GGL + +G+ S + + RY N YP++VY +++ N DC+
Sbjct: 3 GGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYR--YPNQVYYRPVDQYNNQNTFVHDCV 60
Query: 85 KVAI--HTIVTNCTG 97
+ I HT+ T G
Sbjct: 61 NITIKQHTVTTTTKG 75
>pdb|1H0L|A Chain A, Human Prion Protein 121-230 M166cE221C
Length = 112
Score = 26.9 bits (58), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 4/73 (5%)
Query: 29 GGLFMFNVGTLFSAKLYNEAGRY--LYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCIKV 86
GGL + +G+ S + + Y Y YP++VY + N+ DC+ +
Sbjct: 5 GGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPCDEYSNQNNFVHDCVNI 64
Query: 87 AI--HTIVTNCTG 97
I HT+ T G
Sbjct: 65 TIKQHTVTTTTKG 77
>pdb|2LH8|A Chain A, Syrian Hamster Prion Protein With Thiamine
Length = 104
Score = 26.6 bits (57), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 50 RYLYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCIKVAI--HTIVTNCTGA 98
RY N YP++VY +++ N+ DC+ + I HT+ T G
Sbjct: 24 RYYRENMNR--YPNQVYYRPVDQYNNQNNFVHDCVNITIKQHTVTTTTKGE 72
>pdb|1XYQ|A Chain A, Nmr Structure Of The Pig Prion Protein
Length = 111
Score = 26.6 bits (57), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 4/73 (5%)
Query: 29 GGLFMFNVGTLFSAKLYNEAGRY--LYSNATEGDYPDKVYGLYNCRFDVSNDVCQDCIKV 86
GGL + +G+ S L + Y Y YP++VY ++ N DC+ +
Sbjct: 3 GGLGGYMLGSAMSRPLIHFGSDYEDRYYRENMYRYPNQVYYRPVDQYSNQNSFVHDCVNI 62
Query: 87 AI--HTIVTNCTG 97
+ HT+ T G
Sbjct: 63 TVKQHTVTTTTKG 75
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 0.134 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,854,472
Number of Sequences: 62578
Number of extensions: 220491
Number of successful extensions: 412
Number of sequences better than 100.0: 42
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 41
Number of HSP's that attempted gapping in prelim test: 410
Number of HSP's gapped (non-prelim): 43
length of query: 212
length of database: 14,973,337
effective HSP length: 95
effective length of query: 117
effective length of database: 9,028,427
effective search space: 1056325959
effective search space used: 1056325959
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: 49 (23.5 bits)