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= 025436
(253 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2PM7|A Chain A, Crystal Structure Of Yeast Sec1331 EDGE ELEMENT OF THE
Copii Vesicular Coat, Selenomethionine Version
pdb|2PM7|C Chain C, Crystal Structure Of Yeast Sec1331 EDGE ELEMENT OF THE
Copii Vesicular Coat, Selenomethionine Version
Length = 399
Score = 32.0 bits (71), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 21/89 (23%), Positives = 41/89 (46%), Gaps = 4/89 (4%)
Query: 19 VRRCFRPDSPFFASGNIERELLAKQVALDFSEDEKYQLENMVTEDGRRVCCPIVGCNARM 78
+ F+P+ F SGNIE+ + V+ + K LEN + + + N R+
Sbjct: 130 IETNFQPEGDFSLSGNIEQTISKNLVSGNIKSAVKNSLENDLXXEAXVIALD--SNNERL 187
Query: 79 RSLEEFEDHYNARHTASCSVCCRVYPTSR 107
+ E ++ Y A++ + S+ +Y S+
Sbjct: 188 K--ESVKNAYFAKYGSKSSLSRILYSISK 214
>pdb|2PM6|A Chain A, Crystal Structure Of Yeast Sec1331 EDGE ELEMENT OF THE
Copii Vesicular Coat, Native Version
pdb|2PM6|C Chain C, Crystal Structure Of Yeast Sec1331 EDGE ELEMENT OF THE
Copii Vesicular Coat, Native Version
Length = 399
Score = 31.2 bits (69), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 48/105 (45%), Gaps = 7/105 (6%)
Query: 6 DANFESEFPH---WASVRRCFRPDSPFFASGNIERELLAKQVALDFSEDEKYQLENMVTE 62
DAN E E + + F+P+ F SGNIE+ + V+ + K LEN +
Sbjct: 114 DANNEKEDDGEEFFQQIETNFQPEGDFSLSGNIEQTISKNLVSGNIKSAVKNSLENDLLM 173
Query: 63 DGRRVCCPIVGCNARMRSLEEFEDHYNARHTASCSVCCRVYPTSR 107
+ + + N R++ E ++ Y A++ + S+ +Y S+
Sbjct: 174 EA--MVIALDSNNERLK--ESVKNAYFAKYGSKSSLSRILYSISK 214
>pdb|2WD0|A Chain A, Crystal Structure Of Nonsyndromic Deafness (Dfnb12)
Associated Mutant D124g Of Mouse Cadherin-23 Ec1-2
pdb|2WD0|C Chain C, Crystal Structure Of Nonsyndromic Deafness (Dfnb12)
Associated Mutant D124g Of Mouse Cadherin-23 Ec1-2
pdb|4AQA|A Chain A, Crystal Structure Of Deafness Associated Mutant Mouse
Cadherin-23 Ec1-2d124g And Protocadherin-15 Ec1-2 Form I
Length = 214
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 2/67 (2%)
Query: 17 ASVRRCFRPDSPFFASGNIERELLAKQVALDFSEDEKYQLE-NMVTEDGRRVCCPIVGCN 75
SV F+P SPFFA + R ++ LD+ + YQL N +D R +
Sbjct: 143 GSVLYSFQPPSPFFAIDS-ARGIVTVIQELDYEVTQAYQLTVNATDQDKTRPLSTLANLA 201
Query: 76 ARMRSLE 82
+ LE
Sbjct: 202 IIITDLE 208
>pdb|2WCP|A Chain A, Crystal Structure Of Mouse Cadherin-23 Ec1-2
pdb|2WHV|A Chain A, Crystal Structure Of Mouse Cadherin-23 Ec1-2 (all Cation
Binding Sites Occupied By Calcium)
pdb|4APX|A Chain A, Crystal Structure Of Mouse Cadherin-23 Ec1-2 And
Protocadherin-15 Ec1-2 Form I
pdb|4AQ8|A Chain A, Crystal Structure Of Mouse Cadherin-23 Ec1-2 And
Protocadherin-15 Ec1-2 Form Ii
pdb|4AQ8|B Chain B, Crystal Structure Of Mouse Cadherin-23 Ec1-2 And
Protocadherin-15 Ec1-2 Form Ii
pdb|4AXW|A Chain A, Crystal Structure Of Mouse Cadherin-23 Ec1-2 And
Protocadherin-15 Ec1-2, Form I 2.2a
Length = 214
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 2/67 (2%)
Query: 17 ASVRRCFRPDSPFFASGNIERELLAKQVALDFSEDEKYQLE-NMVTEDGRRVCCPIVGCN 75
SV F+P SPFFA + R ++ LD+ + YQL N +D R +
Sbjct: 143 GSVLYSFQPPSPFFAIDS-ARGIVTVIQELDYEVTQAYQLTVNATDQDKTRPLSTLANLA 201
Query: 76 ARMRSLE 82
+ LE
Sbjct: 202 IIITDLE 208
>pdb|4AQE|A Chain A, Crystal Structure Of Deafness Associated Mutant Mouse
Cadherin-23 Ec1-2s70p And Protocadherin-15 Ec1-2 Form I
Length = 214
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 2/67 (2%)
Query: 17 ASVRRCFRPDSPFFASGNIERELLAKQVALDFSEDEKYQLE-NMVTEDGRRVCCPIVGCN 75
SV F+P SPFFA + R ++ LD+ + YQL N +D R +
Sbjct: 143 GSVLYSFQPPSPFFAIDS-ARGIVTVIQELDYEVTQAYQLTVNATDQDKTRPLSTLANLA 201
Query: 76 ARMRSLE 82
+ LE
Sbjct: 202 IIITDLE 208
>pdb|2RGH|A Chain A, Structure Of Alpha-Glycerophosphate Oxidase From
Streptococcus Sp.: A Template For The Mitochondrial
Alpha- Glycerophosphate Dehydrogenase
Length = 571
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 4/58 (6%)
Query: 104 PTSRLLSIHVSEAHDSF--FQAKVARGYPMYECLVEGCGLKFKNYKSRQQHLVDKHKF 159
P LL I+ E +F F KVA +Y+ L G K++NY + ++++ F
Sbjct: 113 PDPXLLPIYEDEGATTFNXFSVKVAXD--LYDKLANVTGTKYENYTLTPEEVLEREPF 168
>pdb|2RGO|A Chain A, Structure Of Alpha-Glycerophosphate Oxidase From
Streptococcus Sp.: A Template For The Mitochondrial
Alpha- Glycerophosphate Dehydrogenase
pdb|2RGO|B Chain B, Structure Of Alpha-Glycerophosphate Oxidase From
Streptococcus Sp.: A Template For The Mitochondrial
Alpha- Glycerophosphate Dehydrogenase
Length = 607
Score = 28.1 bits (61), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 14/56 (25%), Positives = 25/56 (44%)
Query: 104 PTSRLLSIHVSEAHDSFFQAKVARGYPMYECLVEGCGLKFKNYKSRQQHLVDKHKF 159
P LL I+ E +F V +Y+ L G K++NY + ++++ F
Sbjct: 99 PDPMLLPIYEDEGATTFNMFSVKVAMDLYDKLANVTGTKYENYTLTPEEVLEREPF 154
>pdb|2LVH|A Chain A, Solution Structure Of The Zinc Finger Afv1p06 Protein From
The Hyperthermophilic Archaeal Virus Afv1
Length = 59
Score = 28.1 bits (61), Expect = 5.1, Method: Composition-based stats.
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 3/40 (7%)
Query: 131 MYECLVEGCGLKFKNYKSRQQHLVDKHKF-PTSFEFFKKA 169
+Y+CL CGL F+ K +HLV+ K P S +++ ++
Sbjct: 10 VYQCL--RCGLTFRTKKQLIRHLVNTEKVNPLSIDYYYQS 47
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
0.322 0.133 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,524,345
Number of Sequences: 62578
Number of extensions: 217582
Number of successful extensions: 423
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 415
Number of HSP's gapped (non-prelim): 21
length of query: 253
length of database: 14,973,337
effective HSP length: 97
effective length of query: 156
effective length of database: 8,903,271
effective search space: 1388910276
effective search space used: 1388910276
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: 50 (23.9 bits)