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= 000378
(1605 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MKR|B Chain B, Crystal Structure Of Yeast AlphaEPSILON-Cop Subcomplex Of
The Copi Vesicular Coat
Length = 320
Score = 37.0 bits (84), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 37/165 (22%), Positives = 74/165 (44%), Gaps = 16/165 (9%)
Query: 1418 LALAKDHSRGADVKAQATICAQYKIAVTLLQEILRLQKVQGPSAAISAKDEMARLSRHLG 1477
L + + A+ + TIC +Y + +++ E +L P + + + ++ +
Sbjct: 134 LLVVDNKQEIAEAQQLITICREYIVGLSMETERKKL-----PKETLEQQKRICEMAAYFT 188
Query: 1478 SLPLQTKHRINCIRTAIKRNMEVQNY----AYAKQMLELLLSKAPASKQDELRSLIDMCV 1533
LQ H I +RTA+ +++N+ A+A+++LE L P Q + R ++ C
Sbjct: 189 HSNLQPVHMILVLRTALNLFFKLKNFRTAAAFARRLLE--LGPKPEVAQ-QTRKILSACE 245
Query: 1534 QRGLSNKSID-PLEDPSQFCAATLSRLSTIGYDV--CDLCGAKFS 1575
+ ++ + +P CAA+ + G V C L GA +S
Sbjct: 246 KNPTDAYQLNYDMHNPFDICAASYRPIYR-GKPVEKCPLSGACYS 289
>pdb|2YNO|A Chain A, Yeast Betaprime Cop 1-304h6
pdb|2YNO|B Chain B, Yeast Betaprime Cop 1-304h6
Length = 310
Score = 32.3 bits (72), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 165 HPRLPVLYVAYADGLIRAYNIHTYAVHYTLQLDNTIKLLGAGAFAFHPT 213
HP LP++ DG ++ +N TY V TL + L + A HPT
Sbjct: 237 HPTLPIIISGSEDGTLKIWNSSTYKVEKTLN----VGLERSWCIATHPT 281
Score = 30.4 bits (67), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 48/209 (22%), Positives = 88/209 (42%), Gaps = 22/209 (10%)
Query: 47 FDTLTGSRIASIDINSPVVR-MAYSPTSGHAVVAILEDCTIRSCDFDTEQSFVLHSPEKK 105
F+ TG ++ + + +R +A PT + V++ +D T++ ++ E ++ L +
Sbjct: 82 FNYNTGEKVVDFEAHPDYIRSIAVHPTKPY-VLSGSDDLTVKLWNW--ENNWALEQTFEG 138
Query: 106 MESISVDTEVHLALTPLQPVVFFGFHRRMSVTVVGTVEGGRAPTKIKTDLKKPIVNLACH 165
E + +A P P F +V V G P T ++ VN +
Sbjct: 139 HEHFVM----CVAFNPKDPSTFASGCLDRTVKVWSL--GQSTPNFTLTTGQERGVNYVDY 192
Query: 166 ---PRLPVLYVAYADGLIRAYNIHTYAVHYTLQLDNTIKLLGAGAFA-FHPTLEWLFVGD 221
P P + A D I+ ++ T + TL+ + +FA FHPTL + G
Sbjct: 193 YPLPDKPYMITASDDLTIKIWDYQTKSCVATLE-----GHMSNVSFAVFHPTLPIIISGS 247
Query: 222 RRGTLLAWDVS---IERPSMIGMDGSLQV 247
GTL W+ S +E+ +G++ S +
Sbjct: 248 EDGTLKIWNSSTYKVEKTLNVGLERSWCI 276
>pdb|2YNN|A Chain A, Yeast Betaprime Cop 1-304 With Ktktn Motif
Length = 304
Score = 32.3 bits (72), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 165 HPRLPVLYVAYADGLIRAYNIHTYAVHYTLQLDNTIKLLGAGAFAFHPT 213
HP LP++ DG ++ +N TY V TL + L + A HPT
Sbjct: 237 HPTLPIIISGSEDGTLKIWNSSTYKVEKTLN----VGLERSWCIATHPT 281
Score = 30.4 bits (67), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 48/209 (22%), Positives = 88/209 (42%), Gaps = 22/209 (10%)
Query: 47 FDTLTGSRIASIDINSPVVR-MAYSPTSGHAVVAILEDCTIRSCDFDTEQSFVLHSPEKK 105
F+ TG ++ + + +R +A PT + V++ +D T++ ++ E ++ L +
Sbjct: 82 FNYNTGEKVVDFEAHPDYIRSIAVHPTKPY-VLSGSDDLTVKLWNW--ENNWALEQTFEG 138
Query: 106 MESISVDTEVHLALTPLQPVVFFGFHRRMSVTVVGTVEGGRAPTKIKTDLKKPIVNLACH 165
E + +A P P F +V V G P T ++ VN +
Sbjct: 139 HEHFVM----CVAFNPKDPSTFASGCLDRTVKVWSL--GQSTPNFTLTTGQERGVNYVDY 192
Query: 166 ---PRLPVLYVAYADGLIRAYNIHTYAVHYTLQLDNTIKLLGAGAFA-FHPTLEWLFVGD 221
P P + A D I+ ++ T + TL+ + +FA FHPTL + G
Sbjct: 193 YPLPDKPYMITASDDLTIKIWDYQTKSCVATLE-----GHMSNVSFAVFHPTLPIIISGS 247
Query: 222 RRGTLLAWDVS---IERPSMIGMDGSLQV 247
GTL W+ S +E+ +G++ S +
Sbjct: 248 EDGTLKIWNSSTYKVEKTLNVGLERSWCI 276
>pdb|3MKQ|A Chain A, Crystal Structure Of Yeast AlphaBETAPRIME-Cop Subcomplex
Of The Copi Vesicular Coat
pdb|3MKQ|C Chain C, Crystal Structure Of Yeast AlphaBETAPRIME-Cop Subcomplex
Of The Copi Vesicular Coat
pdb|3MKQ|E Chain E, Crystal Structure Of Yeast AlphaBETAPRIME-Cop Subcomplex
Of The Copi Vesicular Coat
Length = 814
Score = 32.3 bits (72), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 165 HPRLPVLYVAYADGLIRAYNIHTYAVHYTLQLDNTIKLLGAGAFAFHPT 213
HP LP++ DG ++ +N TY V TL + L + A HPT
Sbjct: 237 HPTLPIIISGSEDGTLKIWNSSTYKVEKTLN----VGLERSWCIATHPT 281
Score = 31.2 bits (69), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 48/206 (23%), Positives = 87/206 (42%), Gaps = 22/206 (10%)
Query: 47 FDTLTGSRIASIDINSPVVR-MAYSPTSGHAVVAILEDCTIRSCDFDTEQSFVLHSPEKK 105
F+ TG ++ + + +R +A PT + V++ +D T++ ++ E ++ L +
Sbjct: 82 FNYNTGEKVVDFEAHPDYIRSIAVHPTKPY-VLSGSDDLTVKLWNW--ENNWALEQTFEG 138
Query: 106 MESISVDTEVHLALTPLQPVVFFGFHRRMSVTVVGTVEGGRAPTKIKTDLKKPIVNLACH 165
E + +A P P F +V V G P T ++ VN +
Sbjct: 139 HEHFVM----CVAFNPKDPSTFASGCLDRTVKVWSL--GQSTPNFTLTTGQERGVNYVDY 192
Query: 166 ---PRLPVLYVAYADGLIRAYNIHTYAVHYTLQLDNTIKLLGAGAFA-FHPTLEWLFVGD 221
P P + A D I+ ++ T + TL+ + +FA FHPTL + G
Sbjct: 193 YPLPDKPYMITASDDLTIKIWDYQTKSCVATLE-----GHMSNVSFAVFHPTLPIIISGS 247
Query: 222 RRGTLLAWDVS---IERPSMIGMDGS 244
GTL W+ S +E+ +G++ S
Sbjct: 248 EDGTLKIWNSSTYKVEKTLNVGLERS 273
>pdb|2YNP|A Chain A, Yeast Betaprime Cop 1-604 With Ktktn Motif
Length = 604
Score = 32.0 bits (71), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 165 HPRLPVLYVAYADGLIRAYNIHTYAVHYTLQLDNTIKLLGAGAFAFHPT 213
HP LP++ DG ++ +N TY V TL + L + A HPT
Sbjct: 237 HPTLPIIISGSEDGTLKIWNSSTYKVEKTLN----VGLERSWCIATHPT 281
Score = 30.4 bits (67), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 48/209 (22%), Positives = 88/209 (42%), Gaps = 22/209 (10%)
Query: 47 FDTLTGSRIASIDINSPVVR-MAYSPTSGHAVVAILEDCTIRSCDFDTEQSFVLHSPEKK 105
F+ TG ++ + + +R +A PT + V++ +D T++ ++ E ++ L +
Sbjct: 82 FNYNTGEKVVDFEAHPDYIRSIAVHPTKPY-VLSGSDDLTVKLWNW--ENNWALEQTFEG 138
Query: 106 MESISVDTEVHLALTPLQPVVFFGFHRRMSVTVVGTVEGGRAPTKIKTDLKKPIVNLACH 165
E + +A P P F +V V G P T ++ VN +
Sbjct: 139 HEHFVM----CVAFNPKDPSTFASGCLDRTVKVWSL--GQSTPNFTLTTGQERGVNYVDY 192
Query: 166 ---PRLPVLYVAYADGLIRAYNIHTYAVHYTLQLDNTIKLLGAGAFA-FHPTLEWLFVGD 221
P P + A D I+ ++ T + TL+ + +FA FHPTL + G
Sbjct: 193 YPLPDKPYMITASDDLTIKIWDYQTKSCVATLE-----GHMSNVSFAVFHPTLPIIISGS 247
Query: 222 RRGTLLAWDVS---IERPSMIGMDGSLQV 247
GTL W+ S +E+ +G++ S +
Sbjct: 248 EDGTLKIWNSSTYKVEKTLNVGLERSWCI 276
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 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 45,537,072
Number of Sequences: 62578
Number of extensions: 1869842
Number of successful extensions: 4004
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 3993
Number of HSP's gapped (non-prelim): 19
length of query: 1605
length of database: 14,973,337
effective HSP length: 112
effective length of query: 1493
effective length of database: 7,964,601
effective search space: 11891149293
effective search space used: 11891149293
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: 58 (26.9 bits)