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= 001803
(1011 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1W63|B Chain B, Ap1 Clathrin Adaptor Core
pdb|1W63|D Chain D, Ap1 Clathrin Adaptor Core
pdb|1W63|F Chain F, Ap1 Clathrin Adaptor Core
pdb|1W63|H Chain H, Ap1 Clathrin Adaptor Core
pdb|1W63|J Chain J, Ap1 Clathrin Adaptor Core
pdb|1W63|L Chain L, Ap1 Clathrin Adaptor Core
Length = 584
Score = 93.6 bits (231), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 85/308 (27%), Positives = 133/308 (43%), Gaps = 27/308 (8%)
Query: 213 TSPLLWSHNSAVVLAAAGVHW----IMSPKED-----VKRIVKPLLFILRSSGASKYVVL 263
+P L NSAVVL+A V ++S D +K++ PL+ +L + +YV L
Sbjct: 244 VTPRLSHANSAVVLSAVKVLMKFMEMLSKDLDYYATLLKKLAPPLVTLLSAEPEPQYVPL 303
Query: 264 CNIQVFAKALPHLFVPHYEDFFVSSSDSYQSKALKXXXXXXXXXXXXXXXXFKEFQDYIR 323
NI + + P + + FFV +D K K E ++Y
Sbjct: 304 RNINLIVQKRPEILKHEMKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKEYAT 363
Query: 324 DPDRRFAADTVAAIGLCARKLPKMANTCVEGLLALIRQELLTSDIESGNGEADVLXXXXX 383
+ D F V AIG CA K+ + A CV LL LI+ ++ E+ D+
Sbjct: 364 EVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIKDIFRKY-- 421
Query: 384 XXXXXXXXDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKY 443
P+ +E VI L +LDS PEAR +IW+VGEY+ +L + L
Sbjct: 422 ---------PNKYESVIATLCENLDSDDEPEARAAMIWIVGEYAERSDNADELLESFLD- 471
Query: 444 LAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARF 503
F E+ + +LQ+L +K+ L + ++ S L + D N D+RDR
Sbjct: 472 ---GFHDESTQVQLQLLTAIVKLFLKKPTETQELVQQVLS--LATQDSD-NPDLRDRGYI 525
Query: 504 FKKLFSHN 511
+ +L S +
Sbjct: 526 YWRLLSTD 533
Score = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 31/121 (25%), Positives = 54/121 (44%), Gaps = 6/121 (4%)
Query: 1 MAGIRLHVISPLVLVAVGKCARDPSVFVRKCAANALPKLHELRQEEIT-SAIEEIVGILL 59
M IR+ I+ + + KC +D +VRK AA + KLH++ + + + + L+
Sbjct: 110 MGCIRVDKITEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDTLKDLI 169
Query: 60 NDRSPGVVGXXXXXXXSIC-----PNNFTLIGRNYRNLCQILPDVEEWGQILLIEILLRY 114
+D +P VV I N L ++ L L + EW QI +++ L Y
Sbjct: 170 SDSNPMVVANRVAALSEIAESHPSSNLLDLKAQSINKLLTALNECTEWAQIFILDCLGNY 229
Query: 115 V 115
+
Sbjct: 230 M 230
>pdb|2XA7|B Chain B, Ap2 Clathrin Adaptor Core In Active Complex With Cargo
Peptides
Length = 592
Score = 92.4 bits (228), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 82/306 (26%), Positives = 132/306 (43%), Gaps = 27/306 (8%)
Query: 213 TSPLLWSHNSAVVLAAAGV---HWIMSPKED------VKRIVKPLLFILRSSGASKYVVL 263
+P L NSAVVL+A V + PK+ +K++ PL+ +L +YV L
Sbjct: 244 VTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKLAPPLVTLLSGEPEVQYVAL 303
Query: 264 CNIQVFAKALPHLFVPHYEDFFVSSSDSYQSKALKXXXXXXXXXXXXXXXXFKEFQDYIR 323
NI + + P + + FFV +D K K E ++Y
Sbjct: 304 RNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKEYAT 363
Query: 324 DPDRRFAADTVAAIGLCARKLPKMANTCVEGLLALIRQELLTSDIESGNGEADVLXXXXX 383
+ D F V AIG CA K+ + A CV LL LI+ ++ E+ D+
Sbjct: 364 EVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRKY-- 421
Query: 384 XXXXXXXXDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKY 443
P+ +E +I L +LDS+ P+AR +IW+VGEY+ +L + L+
Sbjct: 422 ---------PNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLE- 471
Query: 444 LAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARF 503
F E+ + +L +L +K+ L + ++ S L + D N D+RDR
Sbjct: 472 ---GFHDESTQVQLTLLTAIVKLFLKKPSETQELVQQVLS--LATQDSD-NPDLRDRGYI 525
Query: 504 FKKLFS 509
+ +L S
Sbjct: 526 YWRLLS 531
Score = 44.3 bits (103), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 34/120 (28%), Positives = 55/120 (45%), Gaps = 6/120 (5%)
Query: 1 MAGIRLHVISPLVLVAVGKCARDPSVFVRKCAANALPKLHELRQEEIT-SAIEEIVGILL 59
M IR+ I+ + + KC +D +VRK AA + KLH++ + + + + L+
Sbjct: 110 MGCIRVDKITEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLI 169
Query: 60 NDRSPGVVGXXXXXXXSIC---PNN--FTLIGRNYRNLCQILPDVEEWGQILLIEILLRY 114
D +P VV I PN+ L +N L L + EWGQI +++ L Y
Sbjct: 170 ADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQIFILDCLSNY 229
>pdb|2VGL|B Chain B, Ap2 Clathrin Adaptor Core
pdb|2JKR|B Chain B, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
Phosphos)qikrllse
pdb|2JKR|E Chain E, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
Phosphos)qikrllse
pdb|2JKT|B Chain B, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
Phosphos)eikrllse Q To E Mutant
pdb|2JKT|E Chain E, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
Phosphos)eikrllse Q To E Mutant
Length = 591
Score = 92.4 bits (228), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 82/306 (26%), Positives = 132/306 (43%), Gaps = 27/306 (8%)
Query: 213 TSPLLWSHNSAVVLAAAGV---HWIMSPKED------VKRIVKPLLFILRSSGASKYVVL 263
+P L NSAVVL+A V + PK+ +K++ PL+ +L +YV L
Sbjct: 244 VTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKLAPPLVTLLSGEPEVQYVAL 303
Query: 264 CNIQVFAKALPHLFVPHYEDFFVSSSDSYQSKALKXXXXXXXXXXXXXXXXFKEFQDYIR 323
NI + + P + + FFV +D K K E ++Y
Sbjct: 304 RNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKEYAT 363
Query: 324 DPDRRFAADTVAAIGLCARKLPKMANTCVEGLLALIRQELLTSDIESGNGEADVLXXXXX 383
+ D F V AIG CA K+ + A CV LL LI+ ++ E+ D+
Sbjct: 364 EVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRKY-- 421
Query: 384 XXXXXXXXDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKY 443
P+ +E +I L +LDS+ P+AR +IW+VGEY+ +L + L+
Sbjct: 422 ---------PNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLE- 471
Query: 444 LAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARF 503
F E+ + +L +L +K+ L + ++ S L + D N D+RDR
Sbjct: 472 ---GFHDESTQVQLTLLTAIVKLFLKKPSETQELVQQVLS--LATQDSD-NPDLRDRGYI 525
Query: 504 FKKLFS 509
+ +L S
Sbjct: 526 YWRLLS 531
Score = 44.3 bits (103), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 34/120 (28%), Positives = 55/120 (45%), Gaps = 6/120 (5%)
Query: 1 MAGIRLHVISPLVLVAVGKCARDPSVFVRKCAANALPKLHELRQEEIT-SAIEEIVGILL 59
M IR+ I+ + + KC +D +VRK AA + KLH++ + + + + L+
Sbjct: 110 MGCIRVDKITEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLI 169
Query: 60 NDRSPGVVGXXXXXXXSIC---PNN--FTLIGRNYRNLCQILPDVEEWGQILLIEILLRY 114
D +P VV I PN+ L +N L L + EWGQI +++ L Y
Sbjct: 170 ADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQIFILDCLSNY 229
>pdb|3LL7|A Chain A, Crystal Structure Of Putative Methyltransferase Pg_1098
From Porphyromonas Gingivalis W83
Length = 410
Score = 31.2 bits (69), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 46/90 (51%), Gaps = 3/90 (3%)
Query: 92 LCQILPDVEEWGQIL-LIEILLRYVVASHGLVKESIMSSLLCIESSHSEK-DVFDVNVAL 149
L ++ P ++ W + L+ + +VVA+HG VKE ++ L + EK + +N+ L
Sbjct: 206 LAKLSPXIDLWDTLQSLLHVQELHVVAAHGEVKELLVRXSLNEATIPPEKVPIHAINLLL 265
Query: 150 EDNGIPSRTYDSELVNLVSRSYIEGLGEYL 179
ED IP + E +S Y + + +Y+
Sbjct: 266 EDTVIPF-IFTXEEERSISIPYTDSIDKYV 294
>pdb|3KEO|A Chain A, Crystal Structure Of A Rex-Family Transcriptional
Regulatory Protein From Streptococcus Agalactiae
Complexed With Nad+
pdb|3KEO|B Chain B, Crystal Structure Of A Rex-Family Transcriptional
Regulatory Protein From Streptococcus Agalactiae
Complexed With Nad+
pdb|3KEQ|A Chain A, Crystal Structure Of A Rex-Family Transcriptional
Regulatory Protein From Streptococcus Agalactiae
Complexed With Nad+
pdb|3KEQ|B Chain B, Crystal Structure Of A Rex-Family Transcriptional
Regulatory Protein From Streptococcus Agalactiae
Complexed With Nad+
pdb|3KET|A Chain A, Crystal Structure Of A Rex-Family Transcriptional
Regulatory Protein From Streptococcus Agalactiae Bound
To A Palindromic Operator
Length = 212
Score = 30.8 bits (68), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 23/47 (48%)
Query: 470 AKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLFSHNLCSQV 516
A G D T+ R FSY EL YDV+ FF ++ + + + V
Sbjct: 41 ALGIDSATVRRDFSYFGELGRRGFGYDVKKLMNFFAEILNDHSTTNV 87
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
0.317 0.134 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,839,427
Number of Sequences: 62578
Number of extensions: 1054723
Number of successful extensions: 2516
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 2495
Number of HSP's gapped (non-prelim): 11
length of query: 1011
length of database: 14,973,337
effective HSP length: 108
effective length of query: 903
effective length of database: 8,214,913
effective search space: 7418066439
effective search space used: 7418066439
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)