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= 031317
(161 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 = 194 bits (493), Expect = 2e-50, Method: Compositional matrix adjust.
Identities = 89/155 (57%), Positives = 117/155 (75%)
Query: 1 MIHFVLLISRQGKVRLTKWYSPYTQKERSKVIRELSGVILTRGPKLCNFVEWRGYKVVYK 60
M+ F+LL SRQGK+RL KWY + KER K++REL V+L R PK+C+F+EWR KVVYK
Sbjct: 1 MMRFMLLFSRQGKLRLQKWYLATSDKERKKMVRELMQVVLARKPKMCSFLEWRDLKVVYK 60
Query: 61 RYASLYFCMCVDQEDNELEILEIIHHYVEILDRYFGSVCELDLIFNFHKAYYILDEILIA 120
RYASLYFC ++ +DNEL LE+IH YVE+LD+YFGSVCELD+IFNF KAY+ILDE L+
Sbjct: 61 RYASLYFCCAIEGQDNELITLELIHRYVELLDKYFGSVCELDIIFNFEKAYFILDEFLMG 120
Query: 121 GELQESSKKTVARLIAAQDSLVETAKEQASSISNI 155
G++Q++SKK+V + I D L E + S + +
Sbjct: 121 GDVQDTSKKSVLKAIEQADLLQEEDESPRSVLEEM 155
>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 = 158 bits (400), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 69/141 (48%), Positives = 100/141 (70%)
Query: 1 MIHFVLLISRQGKVRLTKWYSPYTQKERSKVIRELSGVILTRGPKLCNFVEWRGYKVVYK 60
MI F+L+ +R GK RL KWY + E+ K+I E+ V+ R K NFVE+R +K++Y+
Sbjct: 1 MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYR 60
Query: 61 RYASLYFCMCVDQEDNELEILEIIHHYVEILDRYFGSVCELDLIFNFHKAYYILDEILIA 120
RYA LYFC+CVD DN L LE IH++VE+L+ YF +VCELDL+FNF+K Y ++DE+ +A
Sbjct: 61 RYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLA 120
Query: 121 GELQESSKKTVARLIAAQDSL 141
GE++E+S+ V + + SL
Sbjct: 121 GEIRETSQTKVLKQLLMLQSL 141
>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 = 42.7 bits (99), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 26/100 (26%), Positives = 46/100 (46%), Gaps = 2/100 (2%)
Query: 61 RYASLYFCMCVDQEDNELEILEIIHHYVEILDRYFGSVCELDLIFNFHKAYYILDEILIA 120
+ ++++ Q N + E ++ +++ YFG + E ++ NF Y +LDEIL
Sbjct: 59 KRSNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDF 118
Query: 121 GELQESSKKTVARLIAAQD--SLVETAKEQASSISNIIAQ 158
G Q S + I Q S +T +EQ+ S + Q
Sbjct: 119 GYPQNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQ 158
>pdb|2XA7|M Chain M, Ap2 Clathrin Adaptor Core In Active Complex With Cargo
Peptides
Length = 446
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/100 (26%), Positives = 46/100 (46%), Gaps = 2/100 (2%)
Query: 61 RYASLYFCMCVDQEDNELEILEIIHHYVEILDRYFGSVCELDLIFNFHKAYYILDEILIA 120
+ ++++ Q N + E ++ +++ YFG + E ++ NF Y +LDEIL
Sbjct: 59 KRSNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDF 118
Query: 121 GELQESSKKTVARLIAAQD--SLVETAKEQASSISNIIAQ 158
G Q S + I Q S +T +EQ+ S + Q
Sbjct: 119 GYPQNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQ 158
>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 = 32.7 bits (73), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 21/105 (20%), Positives = 48/105 (45%), Gaps = 1/105 (0%)
Query: 54 GYKVVYKRYASLYFCMCVDQEDNELEILEIIHHYVEILDRYFGSVCELDLIFNFHKAYYI 113
G + ++ ++ +LY + + ++ V++ YF + E + NF Y +
Sbjct: 54 GVRFMWIKHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYEL 113
Query: 114 LDEILIAGELQESSKKTVARLIAAQDSLVET-AKEQASSISNIIA 157
LDE++ G Q + K + I + +ET A ++++N ++
Sbjct: 114 LDELMDFGYPQTTDSKILQEFITQEGHKLETGAPRPPATVTNAVS 158
>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 = 30.4 bits (67), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
Query: 54 GYKVVYKRYASLYFCMCVDQEDNELEILEIIHHYVEILDRYF-GSVCELDLIFNFHKAYY 112
G VVYK LYF + +NEL ++ +++ + L + +V + L+ N +
Sbjct: 64 GLTVVYKSSIDLYFYVIGSSYENELMLMTVLNCLFDSLSQMLRKNVEKRALLENMEGLFL 123
Query: 113 ILDEILIAGELQESSKKTVARLIA 136
+DEI+ G + ES + V +A
Sbjct: 124 AVDEIVDGGVILESDPQQVVHRVA 147
>pdb|2HF6|A Chain A, Solution Structure Of Human Zeta-Cop
Length = 149
Score = 30.4 bits (67), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
Query: 54 GYKVVYKRYASLYFCMCVDQEDNELEILEIIHHYVEILDRYF-GSVCELDLIFNFHKAYY 112
G VVYK LYF + +NEL ++ +++ + L + +V + L+ N +
Sbjct: 64 GLTVVYKSSIDLYFYVIGSSYENELMLMAVLNCLFDSLSQMLRKNVEKRALLENMEGLFL 123
Query: 113 ILDEILIAGELQESSKKTVARLIA 136
+DEI+ G + ES + V +A
Sbjct: 124 AVDEIVDGGVILESDPQQVVHRVA 147
>pdb|2Y35|A Chain A, Crystal Structure Of Xrn1-Substrate Complex
Length = 1140
Score = 29.3 bits (64), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 59 YKRYASLYFCMCVDQEDNELEILEIIHHYVE----ILDRYFGSVCELDLIFNFHKAYYIL 114
++ Y ++ ++ N+ I E+ HHYV +LD Y+ V D + FH +I
Sbjct: 411 FQNYKRNFYRNKFKRDPNDELIEELCHHYVNALQWVLDYYYRGVQSWDWYYPFHYTPFIS 470
Query: 115 D 115
D
Sbjct: 471 D 471
>pdb|1TU5|A Chain A, Crystal Structure Of Bovine Plasma Copper-Containing Amine
Oxidase
pdb|1TU5|B Chain B, Crystal Structure Of Bovine Plasma Copper-Containing Amine
Oxidase
pdb|2PNC|A Chain A, Crystal Structure Of Bovine Plasma Copper-Containing Amine
Oxidase In Complex With Clonidine
pdb|2PNC|B Chain B, Crystal Structure Of Bovine Plasma Copper-Containing Amine
Oxidase In Complex With Clonidine
Length = 746
Score = 29.3 bits (64), Expect = 1.0, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 7/69 (10%)
Query: 40 LTRG---PKLCNFVEWRGYKVVYKRYASLYFCMCVDQEDNELEILEIIHHYVEILDRYFG 96
L RG P L +++W + V + +L+ CV +++ L + H+ + L YFG
Sbjct: 381 LIRGVDCPYLATYMDWH-FVVESQTPKTLHDAFCVFEQNKGLPLRR---HHSDFLSHYFG 436
Query: 97 SVCELDLIF 105
V + L+F
Sbjct: 437 GVAQTVLVF 445
>pdb|4G5E|A Chain A, 2,4,6-Trichlorophenol 4-Monooxygenase
pdb|4G5E|B Chain B, 2,4,6-Trichlorophenol 4-Monooxygenase
pdb|4G5E|C Chain C, 2,4,6-Trichlorophenol 4-Monooxygenase
pdb|4G5E|D Chain D, 2,4,6-Trichlorophenol 4-Monooxygenase
Length = 517
Score = 28.5 bits (62), Expect = 1.7, Method: Composition-based stats.
Identities = 11/51 (21%), Positives = 26/51 (50%), Gaps = 7/51 (13%)
Query: 7 LISRQGKVRLTKWYSPYTQKERSK-------VIRELSGVILTRGPKLCNFV 50
+ + G+ R +W+ Y +++ + ++RE++G R P + N+V
Sbjct: 59 FVDKDGERRTMQWFGHYDKEQLRRKRKYHETIMREMAGASFPRTPDVNNYV 109
>pdb|3L8Q|A Chain A, Structure Analysis Of The Type Ii Cohesin Dyad From The
Adap Scaffoldin Of Acetivibrio Cellulolyticus
pdb|3L8Q|B Chain B, Structure Analysis Of The Type Ii Cohesin Dyad From The
Adap Scaffoldin Of Acetivibrio Cellulolyticus
pdb|3L8Q|C Chain C, Structure Analysis Of The Type Ii Cohesin Dyad From The
Adap Scaffoldin Of Acetivibrio Cellulolyticus
pdb|3L8Q|D Chain D, Structure Analysis Of The Type Ii Cohesin Dyad From The
Adap Scaffoldin Of Acetivibrio Cellulolyticus
Length = 350
Score = 26.2 bits (56), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 3/62 (4%)
Query: 98 VCELDL---IFNFHKAYYILDEILIAGELQESSKKTVARLIAAQDSLVETAKEQASSISN 154
V + DL I NF KAY LD+ A +++ V + ++ + E +S+ N
Sbjct: 79 VADNDLEKGILNFSKAYVSLDDYRTAAAPEQTGTVAVVKFKVLKEETSSISFEDTTSVPN 138
Query: 155 II 156
I
Sbjct: 139 AI 140
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
0.323 0.137 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,351,023
Number of Sequences: 62578
Number of extensions: 165243
Number of successful extensions: 371
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 356
Number of HSP's gapped (non-prelim): 20
length of query: 161
length of database: 14,973,337
effective HSP length: 91
effective length of query: 70
effective length of database: 9,278,739
effective search space: 649511730
effective search space used: 649511730
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 bits)