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= psy12905
(611 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1W63|M Chain M, Ap1 Clathrin Adaptor Core
pdb|1W63|N Chain N, Ap1 Clathrin Adaptor Core
pdb|1W63|O Chain O, Ap1 Clathrin Adaptor Core
pdb|1W63|P Chain P, Ap1 Clathrin Adaptor Core
pdb|1W63|R Chain R, Ap1 Clathrin Adaptor Core
pdb|1W63|V Chain V, Ap1 Clathrin Adaptor Core
Length = 423
Score = 35.4 bits (80), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 19/87 (21%), Positives = 42/87 (48%)
Query: 112 VRYVYQPLEKLYMLLITTKTSNILEDLETLRLFSRVIPEYCRTLDENEVTDNAFSLIFAF 171
VR+++ LY++ + K + + L +V EY + L+E + DN +
Sbjct: 55 VRFMWIKHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELL 114
Query: 172 DEIVALGYRESVNLAQVRTFVEMDSHE 198
DE++ GY ++ + ++ F+ + H+
Sbjct: 115 DELMDFGYPQTTDSKILQEFITQEGHK 141
Score = 29.3 bits (64), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 12/49 (24%), Positives = 26/49 (53%)
Query: 2 EYCRTLDENEVTDNAFSLIFAFDEIVALGYRESVNLAQVRTFVEMDSHE 50
EY + L+E + DN + DE++ GY ++ + ++ F+ + H+
Sbjct: 93 EYFKELEEESIRDNFVIIYELLDELMDFGYPQTTDSKILQEFITQEGHK 141
>pdb|2XDQ|A Chain A, Dark Operative Protochlorophyllide Oxidoreductase (Chln-
Chlb)2 Complex
Length = 460
Score = 32.7 bits (73), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 100 SGKQHTFVETDSVRYVYQPLEKLYMLLITTKTSN-ILEDLETLRLFSRVIPEYCRT-LDE 157
+G HTF V ++YQ +E + L+I TKT L++ + +F+ P Y L+E
Sbjct: 15 TGNYHTFCPISCVAWLYQKIEDSFFLVIGTKTCGYFLQNAMGVMIFAE--PRYAMAELEE 72
Query: 158 NEVT 161
+++
Sbjct: 73 GDIS 76
>pdb|2VGL|S Chain S, Ap2 Clathrin Adaptor Core
pdb|2JKR|I Chain I, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
Phosphos)qikrllse
pdb|2JKR|S Chain S, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
Phosphos)qikrllse
pdb|2JKT|I Chain I, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
Phosphos)eikrllse Q To E Mutant
pdb|2JKT|S Chain S, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
Phosphos)eikrllse Q To E Mutant
pdb|2XA7|S Chain S, Ap2 Clathrin Adaptor Core In Active Complex With Cargo
Peptides
Length = 142
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 24/99 (24%), Positives = 42/99 (42%), Gaps = 1/99 (1%)
Query: 101 GKQHTFVETDSVRYVYQPLEKLYMLLITTKTSNILEDLETLRLFSRVIPEYCRTLDENEV 160
K FVE + + +Y+ LY + N L LE + F V+ EY + E ++
Sbjct: 44 AKHTNFVEFRNFKIIYRRYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDL 103
Query: 161 TDNAFSLIFAFDEIVALG-YRESVNLAQVRTFVEMDSHE 198
N + + DE+ G RE+ ++ + + S E
Sbjct: 104 VFNFYKVYTVVDEMFLAGEIRETSQTKVLKQLLMLQSLE 142
>pdb|1W63|Q Chain Q, Ap1 Clathrin Adaptor Core
pdb|1W63|S Chain S, Ap1 Clathrin Adaptor Core
pdb|1W63|T Chain T, Ap1 Clathrin Adaptor Core
pdb|1W63|U Chain U, Ap1 Clathrin Adaptor Core
pdb|1W63|W Chain W, Ap1 Clathrin Adaptor Core
pdb|1W63|X Chain X, Ap1 Clathrin Adaptor Core
Length = 158
Score = 29.6 bits (65), Expect = 5.1, Method: Composition-based stats.
Identities = 25/107 (23%), Positives = 47/107 (43%), Gaps = 6/107 (5%)
Query: 72 IAIVSRQFVEMTRARIEGLLAAFPKLMSSGKQHTFVETDSVRYVYQPLEKLYMLLITTKT 131
+A ++ +M R ++ +LA PK+ S F+E ++ VY+ LY
Sbjct: 21 LATSDKERKKMVRELMQVVLARKPKMCS------FLEWRDLKVVYKRYASLYFCCAIEGQ 74
Query: 132 SNILEDLETLRLFSRVIPEYCRTLDENEVTDNAFSLIFAFDEIVALG 178
N L LE + + ++ +Y ++ E ++ N F DE + G
Sbjct: 75 DNELITLELIHRYVELLDKYFGSVCELDIIFNFEKAYFILDEFLMGG 121
>pdb|2BP5|M Chain M, Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second Domain),
Complexed With Non-Canonical Internalization Peptide
Vedyeqglsg
pdb|2VGL|M Chain M, Ap2 Clathrin Adaptor Core
pdb|2JKR|M Chain M, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
Phosphos)qikrllse
pdb|2JKR|U Chain U, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
Phosphos)qikrllse
pdb|2JKT|M Chain M, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
Phosphos)eikrllse Q To E Mutant
pdb|2JKT|U Chain U, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
Phosphos)eikrllse Q To E Mutant
Length = 435
Score = 29.6 bits (65), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 122 LYMLLITTKTSNILEDLETLRLFSRVIPEYCRTLDENEVTDNAFSLIFAF-DEIVALGYR 180
+++ +T + N E L V+ Y + E + +N F LI+ DEI+ GY
Sbjct: 63 IWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNN-FVLIYELLDEILDFGYP 121
Query: 181 ESVNLAQVRTFV 192
++ ++TF+
Sbjct: 122 QNSETGALKTFI 133
>pdb|2XA7|M Chain M, Ap2 Clathrin Adaptor Core In Active Complex With Cargo
Peptides
Length = 446
Score = 29.3 bits (64), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 122 LYMLLITTKTSNILEDLETLRLFSRVIPEYCRTLDENEVTDNAFSLIFAF-DEIVALGYR 180
+++ +T + N E L V+ Y + E + +N F LI+ DEI+ GY
Sbjct: 63 IWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNN-FVLIYELLDEILDFGYP 121
Query: 181 ESVNLAQVRTFV 192
++ ++TF+
Sbjct: 122 QNSETGALKTFI 133
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 0.135 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,025,714
Number of Sequences: 62578
Number of extensions: 619529
Number of successful extensions: 1423
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1413
Number of HSP's gapped (non-prelim): 15
length of query: 611
length of database: 14,973,337
effective HSP length: 105
effective length of query: 506
effective length of database: 8,402,647
effective search space: 4251739382
effective search space used: 4251739382
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)