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= psy9047
(110 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4APX|B Chain B, Crystal Structure Of Mouse Cadherin-23 Ec1-2 And
Protocadherin-15 Ec1-2 Form I
pdb|4AQ8|C Chain C, Crystal Structure Of Mouse Cadherin-23 Ec1-2 And
Protocadherin-15 Ec1-2 Form Ii
pdb|4AQ8|D Chain D, Crystal Structure Of Mouse Cadherin-23 Ec1-2 And
Protocadherin-15 Ec1-2 Form Ii
pdb|4AQA|B Chain B, Crystal Structure Of Deafness Associated Mutant Mouse
Cadherin-23 Ec1-2d124g And Protocadherin-15 Ec1-2 Form I
pdb|4AQE|B Chain B, Crystal Structure Of Deafness Associated Mutant Mouse
Cadherin-23 Ec1-2s70p And Protocadherin-15 Ec1-2 Form I
pdb|4AXW|B Chain B, Crystal Structure Of Mouse Cadherin-23 Ec1-2 And
Protocadherin-15 Ec1-2, Form I 2.2a
Length = 242
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 32/95 (33%), Positives = 41/95 (43%), Gaps = 19/95 (20%)
Query: 20 VSDLTPVGSTIFKNLR----AVDADAGVNGLVEYFIVPSQDKNIGTADGVGKDRVTVVDG 75
V++LTPVG+TIF A D D G NG +EY I D D
Sbjct: 136 VNELTPVGTTIFTGFSGDNGATDIDDGPNGQIEYVI------QYNPEDPTSNDT------ 183
Query: 76 YSYFSINLPHQGQVTVNRSLDFEKTQRYLVTIVAS 110
F I L G V + + L++E RY V I A+
Sbjct: 184 ---FEIPLMLTGNVVLRKRLNYEDKTRYYVIIQAN 215
>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 = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 44/96 (45%), Gaps = 23/96 (23%)
Query: 15 PVIVRVSDLTPVGSTIFKNLRAVDADAGVNGLVEYFIVPSQDKNIGTADGVGKDRVTVVD 74
P VR+ + TPVG+ IF + A D D G G V Y P
Sbjct: 114 PYSVRIPENTPVGTPIFI-VNATDPDLGAGGSVLYSFQPPS------------------- 153
Query: 75 GYSYFSINLPHQGQVTVNRSLDFEKTQRYLVTIVAS 110
+F+I+ +G VTV + LD+E TQ Y +T+ A+
Sbjct: 154 --PFFAIDS-ARGIVTVIQELDYEVTQAYQLTVNAT 186
>pdb|3MVS|A Chain A, Structure Of The N-Terminus Of Cadherin 23
Length = 210
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 44/96 (45%), Gaps = 23/96 (23%)
Query: 15 PVIVRVSDLTPVGSTIFKNLRAVDADAGVNGLVEYFIVPSQDKNIGTADGVGKDRVTVVD 74
P VR+ + TPVG+ IF + A D D G G V Y P
Sbjct: 113 PYSVRIPENTPVGTPIFI-VNATDPDLGAGGSVLYSFQPPS------------------- 152
Query: 75 GYSYFSINLPHQGQVTVNRSLDFEKTQRYLVTIVAS 110
+F+I+ +G VTV + LD+E TQ Y +T+ A+
Sbjct: 153 --PFFAID-SARGIVTVIQELDYEVTQAYQLTVNAT 185
>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 = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 44/96 (45%), Gaps = 23/96 (23%)
Query: 15 PVIVRVSDLTPVGSTIFKNLRAVDADAGVNGLVEYFIVPSQDKNIGTADGVGKDRVTVVD 74
P VR+ + TPVG+ IF + A D D G G V Y P
Sbjct: 114 PYSVRIPENTPVGTPIFI-VNATDPDLGAGGSVLYSFQPPS------------------- 153
Query: 75 GYSYFSINLPHQGQVTVNRSLDFEKTQRYLVTIVAS 110
+F+I+ +G VTV + LD+E TQ Y +T+ A+
Sbjct: 154 --PFFAID-SARGIVTVIQELDYEVTQAYQLTVNAT 186
>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 = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 44/96 (45%), Gaps = 23/96 (23%)
Query: 15 PVIVRVSDLTPVGSTIFKNLRAVDADAGVNGLVEYFIVPSQDKNIGTADGVGKDRVTVVD 74
P VR+ + TPVG+ IF + A D D G G V Y P
Sbjct: 114 PYSVRIPENTPVGTPIFI-VNATDPDLGAGGSVLYSFQPPS------------------- 153
Query: 75 GYSYFSINLPHQGQVTVNRSLDFEKTQRYLVTIVAS 110
+F+I+ +G VTV + LD+E TQ Y +T+ A+
Sbjct: 154 --PFFAID-SARGIVTVIQELDYEVTQAYQLTVNAT 186
>pdb|2EE0|A Chain A, Solution Structures Of The Ca Domain Of Human
Protocadherin 9
Length = 114
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 46/99 (46%), Gaps = 26/99 (26%)
Query: 16 VIVRVSDLTPVGSTIFKNLRAVDADAGVNGLVEYF----IVPSQDKNIGTADGVGKDRVT 71
V V + + PVG+++ + L A DAD G N + Y + P+ +
Sbjct: 19 VEVHIPENAPVGTSVIQ-LHATDADIGSNAEIRYIFGAQVAPATKR-------------- 63
Query: 72 VVDGYSYFSINLPHQGQVTVNRSLDFEKTQRYLVTIVAS 110
F++N G +TV RSLD E+T + VT++AS
Sbjct: 64 ------LFALNNT-TGLITVQRSLDREETAIHKVTVLAS 95
>pdb|3UBH|A Chain A, Crystal Structure Of Drosophila N-Cadherin Ec1-4
Length = 419
Score = 28.5 bits (62), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 23/32 (71%), Gaps = 1/32 (3%)
Query: 20 VSDLTPVGSTIFKNLRAVDADAGVNGLVEYFI 51
V + P+G++I + ++A+D+D+G N +EY +
Sbjct: 334 VDEDIPLGTSILR-VKAMDSDSGSNAEIEYLV 364
>pdb|3GF6|A Chain A, Crystal Structure Of A Bacterial Lipoprotein (Bt_1233)
From Bacteroides Thetaiotaomicron Vpi-5482 At 1.69 A
Resolution
pdb|3GF6|B Chain B, Crystal Structure Of A Bacterial Lipoprotein (Bt_1233)
From Bacteroides Thetaiotaomicron Vpi-5482 At 1.69 A
Resolution
Length = 224
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 54 SQDKNIGTADGVGKDRVTVVDGYSYFSINLPHQGQVTVNRSLDFEKTQRYLVTI 107
+D+N+ +GVGK ++T GY N P + QV + S D T +Y V +
Sbjct: 67 QKDQNVADFNGVGKSKLTXSLGYK--DGNYPSESQVPIYTSQDV--TAKYAVKL 116
>pdb|2YST|A Chain A, Solution Structure Of The Third Cadherin Domain From
Human Protocadherin 7
Length = 119
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 27 GSTIFKNLRAVDADAGVNGLVEY 49
G+ I + LRA D D GVNG +EY
Sbjct: 30 GTPILQ-LRAADLDVGVNGQIEY 51
>pdb|1R4V|A Chain A, 1.9a Crystal Structure Of Protein Aq328 From Aquifex
Aeolicus
Length = 171
Score = 26.6 bits (57), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 32 KNLRAVDADAGVNGLVEYF-IVPSQDKNIG 60
KN + ++ D GV+ L+EY +P + N+G
Sbjct: 95 KNFQKIEQDXGVDELLEYIAFIPPVEXNVG 124
>pdb|2PUS|A Chain A, Unprecedented Activation Mechanism Of A Non-Canonical
Rna-Dependent Rna Polymerase
pdb|2QJ1|A Chain A, Crystal Structure Of Infectious Bursal Disease Virus Vp1
Polymerase Incubated With An Oligopeptide Mimicking The
Vp3 C-Terminus
pdb|2R70|A Chain A, Crystal Structure Of Infectious Bursal Disease Virus Vp1
Polymerase, Cocrystallized With An Oligopeptide
Mimicking The Vp3 C-Terminus.
pdb|2R72|A Chain A, Crystal Structure Of Infectious Bursal Disease Virus Vp1
Polymerase, Incubated With Mg2+ Ion
Length = 852
Score = 26.2 bits (56), Expect = 4.7, Method: Composition-based stats.
Identities = 16/66 (24%), Positives = 33/66 (50%), Gaps = 7/66 (10%)
Query: 41 AGVNGLVEYFIVPSQDKNIGTADGVGKDRVTVVDGYSYFSINLPHQGQVTVNRSLDFEKT 100
G+N +VE+ + P + K + V D + +V +++SI+L +G+ R +
Sbjct: 387 GGLNRIVEWILAPEEPKAL-----VYADNIYIVHSNTWYSIDL-EKGEANCTRQ-HMQAA 439
Query: 101 QRYLVT 106
Y++T
Sbjct: 440 MYYILT 445
>pdb|2PGG|A Chain A, Crystal Structure Of A Birnavirus (Ibdv) Rna-Dependent Rna
Polymerase Vp1
Length = 774
Score = 26.2 bits (56), Expect = 4.7, Method: Composition-based stats.
Identities = 16/66 (24%), Positives = 33/66 (50%), Gaps = 7/66 (10%)
Query: 41 AGVNGLVEYFIVPSQDKNIGTADGVGKDRVTVVDGYSYFSINLPHQGQVTVNRSLDFEKT 100
G+N +VE+ + P + K + V D + +V +++SI+L +G+ R +
Sbjct: 350 GGLNRIVEWILAPEEPKAL-----VYADNIYIVHSNTWYSIDL-EKGEANCTRQ-HMQAA 402
Query: 101 QRYLVT 106
Y++T
Sbjct: 403 MYYILT 408
>pdb|1NCJ|A Chain A, N-Cadherin, Two-Domain Fragment
Length = 215
Score = 25.8 bits (55), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 17/77 (22%)
Query: 36 AVDAD--AGVNGLVEYFIVPSQDKNIGTADGVGKDRVTVVDGYSYFSINLPHQGQVTVNR 93
A+DAD +NG++ Y IV SQ + + + F+IN +TV
Sbjct: 132 AIDADDPNALNGMLRYRIV-SQAPSTPSPN--------------MFTINNETGDIITVAA 176
Query: 94 SLDFEKTQRYLVTIVAS 110
LD EK Q+Y + I A+
Sbjct: 177 GLDREKVQQYTLIIQAT 193
>pdb|3OXO|A Chain A, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
Covalently Bound To Coa
pdb|3OXO|B Chain B, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
Covalently Bound To Coa
pdb|3OXO|C Chain C, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
Covalently Bound To Coa
pdb|3OXO|D Chain D, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
Covalently Bound To Coa
pdb|3OXO|E Chain E, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
Covalently Bound To Coa
pdb|3OXO|F Chain F, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
Covalently Bound To Coa
pdb|3OXO|G Chain G, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
Covalently Bound To Coa
pdb|3OXO|H Chain H, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
Covalently Bound To Coa
Length = 488
Score = 25.8 bits (55), Expect = 6.7, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 37 VDADAGVNGLVEYFIVPSQDKNIGTADGVGKDRVTVVDGYSYFS 80
+ ++ G+ GL Y P Q++ GK+ VTV+ G SYFS
Sbjct: 302 LQSENGILGLGPY---PLQNEVDADLINAGKETVTVLPGASYFS 342
>pdb|1OOZ|A Chain A, Deletion Mutant Of Succinyl-coa:3-ketoacid Coa Transferase
From Pig Heart
pdb|1OOZ|B Chain B, Deletion Mutant Of Succinyl-coa:3-ketoacid Coa Transferase
From Pig Heart
pdb|1OPE|A Chain A, Deletion Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
pdb|1OPE|B Chain B, Deletion Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
Length = 475
Score = 25.8 bits (55), Expect = 6.9, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 37 VDADAGVNGLVEYFIVPSQDKNIGTADGVGKDRVTVVDGYSYFS 80
+ ++ G+ GL Y P Q++ GK+ VTV+ G SYFS
Sbjct: 296 LQSENGILGLGPY---PLQNEVDADLINAGKETVTVLPGASYFS 336
>pdb|1O9L|A Chain A, Succinate:coenzyme-A Transferase (Pig Heart)
pdb|1O9L|B Chain B, Succinate:coenzyme-A Transferase (Pig Heart)
pdb|1O9L|C Chain C, Succinate:coenzyme-A Transferase (Pig Heart)
pdb|1O9L|D Chain D, Succinate:coenzyme-A Transferase (Pig Heart)
pdb|1OOY|A Chain A, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
pdb|1OOY|B Chain B, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
pdb|3K6M|A Chain A, Dynamic Domains Of Succinyl-Coa:3-Ketoacid-Coenzyme A
Transferase From Pig Heart.
pdb|3K6M|D Chain D, Dynamic Domains Of Succinyl-Coa:3-Ketoacid-Coenzyme A
Transferase From Pig Heart.
pdb|3K6M|C Chain C, Dynamic Domains Of Succinyl-Coa:3-Ketoacid-Coenzyme A
Transferase From Pig Heart.
pdb|3K6M|B Chain B, Dynamic Domains Of Succinyl-Coa:3-Ketoacid-Coenzyme A
Transferase From Pig Heart
Length = 481
Score = 25.8 bits (55), Expect = 7.3, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 37 VDADAGVNGLVEYFIVPSQDKNIGTADGVGKDRVTVVDGYSYFS 80
+ ++ G+ GL Y P Q++ GK+ VTV+ G SYFS
Sbjct: 302 LQSENGILGLGPY---PLQNEVDADLINAGKETVTVLPGASYFS 342
>pdb|2NRC|A Chain A, C28a Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
pdb|2NRC|B Chain B, C28a Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
pdb|2NRC|C Chain C, C28a Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
pdb|2NRC|D Chain D, C28a Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
Length = 481
Score = 25.4 bits (54), Expect = 7.6, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 37 VDADAGVNGLVEYFIVPSQDKNIGTADGVGKDRVTVVDGYSYFS 80
+ ++ G+ GL Y P Q++ GK+ VTV+ G SYFS
Sbjct: 302 LQSENGILGLGPY---PLQNEVDADLINAGKETVTVLPGASYFS 342
>pdb|2NRB|A Chain A, C28s Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
pdb|2NRB|B Chain B, C28s Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
pdb|2NRB|C Chain C, C28s Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
pdb|2NRB|D Chain D, C28s Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
Length = 481
Score = 25.4 bits (54), Expect = 7.8, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 37 VDADAGVNGLVEYFIVPSQDKNIGTADGVGKDRVTVVDGYSYFS 80
+ ++ G+ GL Y P Q++ GK+ VTV+ G SYFS
Sbjct: 302 LQSENGILGLGPY---PLQNEVDADLINAGKETVTVLPGASYFS 342
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
0.319 0.136 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,026,578
Number of Sequences: 62578
Number of extensions: 115542
Number of successful extensions: 240
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 223
Number of HSP's gapped (non-prelim): 24
length of query: 110
length of database: 14,973,337
effective HSP length: 74
effective length of query: 36
effective length of database: 10,342,565
effective search space: 372332340
effective search space used: 372332340
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)