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= 032296
(143 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 134 bits (336), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 60/135 (44%), Positives = 99/135 (73%)
Query: 3 IRFILMVNKQGQTRLAQYYEWLTLEERRALEGEIVRKCLARTEQQCSFVEHRNYKIVYRR 62
+RF+L+ ++QG+ RL ++Y + +ER+ + E+++ LAR + CSF+E R+ K+VY+R
Sbjct: 2 MRFMLLFSRQGKLRLQKWYLATSDKERKKMVRELMQVVLARKPKMCSFLEWRDLKVVYKR 61
Query: 63 YASLFFLVGVDNDENELAILEFIHLLVETMDRHFGNVCELDIMFHLEKAHFMLEEMVMNG 122
YASL+F ++ +NEL LE IH VE +D++FG+VCELDI+F+ EKA+F+L+E +M G
Sbjct: 62 YASLYFCCAIEGQDNELITLELIHRYVELLDKYFGSVCELDIIFNFEKAYFILDEFLMGG 121
Query: 123 CIVETSKSNILSPIQ 137
+ +TSK ++L I+
Sbjct: 122 DVQDTSKKSVLKAIE 136
>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 = 118 bits (295), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 58/140 (41%), Positives = 94/140 (67%)
Query: 3 IRFILMVNKQGQTRLAQYYEWLTLEERRALEGEIVRKCLARTEQQCSFVEHRNYKIVYRR 62
IRFIL+ N+ G+TRLA++Y +E++ L E+ R + +FVE RN+KI+YRR
Sbjct: 2 IRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRR 61
Query: 63 YASLFFLVGVDNDENELAILEFIHLLVETMDRHFGNVCELDIMFHLEKAHFMLEEMVMNG 122
YA L+F + VD ++N LA LE IH VE ++ +F NVCELD++F+ K + +++EM + G
Sbjct: 62 YAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAG 121
Query: 123 CIVETSKSNILSPIQLMEKM 142
I ETS++ +L + +++ +
Sbjct: 122 EIRETSQTKVLKQLLMLQSL 141
>pdb|3TJZ|C Chain C, Crystal Structure Of Arf1 Bound To The GammaZETA-Cop Core
Complex
pdb|3TJZ|F Chain F, Crystal Structure Of Arf1 Bound To The GammaZETA-Cop Core
Complex
Length = 153
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 33/139 (23%), Positives = 75/139 (53%), Gaps = 6/139 (4%)
Query: 3 IRFILMVNKQGQTRLAQYYE--WLTLEERRALEGEIVRKCLARTEQQCSFVEHRNYKIVY 60
++ IL+++ G A+YY+ + +++E++A E I K RT+ + + +E +VY
Sbjct: 13 VKAILILDNDGDRLFAKYYDDTYPSVKEQKAFEKNIFNKT-HRTDSEIALLE--GLTVVY 69
Query: 61 RRYASLFFLVGVDNDENELAILEFIHLLVETMDRHF-GNVCELDIMFHLEKAHFMLEEMV 119
+ L+F V + ENEL ++ ++ L +++ + NV + ++ ++E ++E+V
Sbjct: 70 KSSIDLYFYVIGSSYENELMLMTVLNCLFDSLSQMLRKNVEKRALLENMEGLFLAVDEIV 129
Query: 120 MNGCIVETSKSNILSPIQL 138
G I+E+ ++ + L
Sbjct: 130 DGGVILESDPQQVVHRVAL 148
>pdb|2HF6|A Chain A, Solution Structure Of Human Zeta-Cop
Length = 149
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 33/139 (23%), Positives = 75/139 (53%), Gaps = 6/139 (4%)
Query: 3 IRFILMVNKQGQTRLAQYYE--WLTLEERRALEGEIVRKCLARTEQQCSFVEHRNYKIVY 60
++ IL+++ G A+YY+ + +++E++A E I K RT+ + + +E +VY
Sbjct: 13 VKAILILDNDGDRLFAKYYDDTYPSVKEQKAFEKNIFNKT-HRTDSEIALLE--GLTVVY 69
Query: 61 RRYASLFFLVGVDNDENELAILEFIHLLVETMDRHF-GNVCELDIMFHLEKAHFMLEEMV 119
+ L+F V + ENEL ++ ++ L +++ + NV + ++ ++E ++E+V
Sbjct: 70 KSSIDLYFYVIGSSYENELMLMAVLNCLFDSLSQMLRKNVEKRALLENMEGLFLAVDEIV 129
Query: 120 MNGCIVETSKSNILSPIQL 138
G I+E+ ++ + L
Sbjct: 130 DGGVILESDPQQVVHRVAL 148
>pdb|3CKC|A Chain A, B. Thetaiotaomicron Susd
pdb|3CKC|B Chain B, B. Thetaiotaomicron Susd
Length = 527
Score = 26.6 bits (57), Expect = 4.7, Method: Composition-based stats.
Identities = 18/44 (40%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 42 ARTEQQCSFVEHRNYKIVYRRYASLFFLVGVDNDENELAILEFI 85
A+ E+ S V YK+ Y+ LF DNDENE A+ E I
Sbjct: 220 AKAEEYASKVIGSAYKLC-TNYSELFM---ADNDENENAMQEII 259
>pdb|3CK7|A Chain A, B. Thetaiotaomicron Susd With Alpha-Cyclodextrin
pdb|3CK7|B Chain B, B. Thetaiotaomicron Susd With Alpha-Cyclodextrin
pdb|3CK7|C Chain C, B. Thetaiotaomicron Susd With Alpha-Cyclodextrin
pdb|3CK7|D Chain D, B. Thetaiotaomicron Susd With Alpha-Cyclodextrin
pdb|3CK8|A Chain A, B. Thetaiotaomicron Susd With Beta-Cyclodextrin
pdb|3CK8|B Chain B, B. Thetaiotaomicron Susd With Beta-Cyclodextrin
pdb|3CKB|A Chain A, B. Thetaiotaomicron Susd With Maltotriose
pdb|3CKB|B Chain B, B. Thetaiotaomicron Susd With Maltotriose
pdb|3CK9|A Chain A, B. Thetaiotaomicron Susd With Maltoheptaose
pdb|3CK9|B Chain B, B. Thetaiotaomicron Susd With Maltoheptaose
Length = 527
Score = 26.6 bits (57), Expect = 4.7, Method: Composition-based stats.
Identities = 18/44 (40%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 42 ARTEQQCSFVEHRNYKIVYRRYASLFFLVGVDNDENELAILEFI 85
A+ E+ S V YK+ Y+ LF DNDENE A+ E I
Sbjct: 220 AKAEEYASKVIGSAYKLC-TNYSELFM---ADNDENENAMQEII 259
>pdb|3O7P|A Chain A, Crystal Structure Of The E.Coli Fucose:proton Symporter,
Fucp (N162a)
Length = 438
Score = 26.2 bits (56), Expect = 6.5, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 52 EHRNYKIVYRRYASLFFLVGVDNDENELAILEF 84
+ R+Y I + SLFFL V N+ N++ + +F
Sbjct: 20 QSRSYIIPFALLCSLFFLWAVANNLNDILLPQF 52
>pdb|3O7Q|A Chain A, Crystal Structure Of A Major Facilitator Superfamily
(Mfs) Transporter, Fucp, In The Outward Conformation
Length = 438
Score = 26.2 bits (56), Expect = 6.5, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 52 EHRNYKIVYRRYASLFFLVGVDNDENELAILEF 84
+ R+Y I + SLFFL V N+ N++ + +F
Sbjct: 20 QSRSYIIPFALLCSLFFLWAVANNLNDILLPQF 52
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
0.327 0.139 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,750,511
Number of Sequences: 62578
Number of extensions: 132713
Number of successful extensions: 385
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 378
Number of HSP's gapped (non-prelim): 12
length of query: 143
length of database: 14,973,337
effective HSP length: 89
effective length of query: 54
effective length of database: 9,403,895
effective search space: 507810330
effective search space used: 507810330
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 46 (22.3 bits)