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= 004562
(745 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4HG6|A Chain A, Structure Of A Cellulose Synthase - Cellulose
Translocation Intermediate
Length = 802
Score = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 43/180 (23%), Positives = 76/180 (42%), Gaps = 14/180 (7%)
Query: 425 ASCSYEHQTKWGEEVGFSYQSVSEDFFTGFILHCKGWTSTYLDPSRPQFLGTSTTNLNDV 484
S + + E GF+ ++++ED T +H +GW S Y+D R G
Sbjct: 319 GSAAVLRRRALDEAGGFAGETITEDAETALEIHSRGWKSLYID--RAMIAGLQPETFASF 376
Query: 485 LIQGTRWASGLIDVSISRFCPLLYGPSRMSLLLSMCY-GEMS--LFPLLYCLPLWCFATL 541
+ Q RWA+G++ + + + G + + +CY MS FPL+ + F
Sbjct: 377 IQQRGRWATGMMQMLLLKNPLFRRG---LGIAQRLCYLNSMSFWFFPLVRMM----FLVA 429
Query: 542 PQLCLLNGIPLYPETI--VFSLLPQVSSPFFMVFSFIFLSAICKHLQEVISTGGSVYTWR 599
P + L GI ++ T V + +P + F+V + +F + EV + Y R
Sbjct: 430 PLIYLFFGIEIFVATFEEVLAYMPGYLAVSFLVQNALFARQRWPLVSEVYEVAQAPYLAR 489
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 42/87 (48%), Gaps = 5/87 (5%)
Query: 55 LLVFASELLLSFIWLLGRAYLWRPVSRTVFPERLPEDDKLPAIDVFICTADPEKEPTFGV 114
LL+FA E I+ L P R FP L + ++LP +D+ + + + EP +
Sbjct: 102 LLLFAVETFSISIFFLNGFLSADPTDRP-FPRPL-QPEELPTVDILVPSYN---EPADML 156
Query: 115 MNTVLSAMALDYPVDKLHVYLSDDGGS 141
T+ +A + YP V L DDGG+
Sbjct: 157 SVTLAAAKNMIYPARLRTVVLCDDGGT 183
>pdb|3K2B|A Chain A, Crystal Structure Of Photosynthetic A4 Isoform
Glyceraldehyde-3- Phosphate Dehydrogenase Complexed With
Nad, From Arabidopsis Thaliana
pdb|3K2B|B Chain B, Crystal Structure Of Photosynthetic A4 Isoform
Glyceraldehyde-3- Phosphate Dehydrogenase Complexed With
Nad, From Arabidopsis Thaliana
pdb|3K2B|C Chain C, Crystal Structure Of Photosynthetic A4 Isoform
Glyceraldehyde-3- Phosphate Dehydrogenase Complexed With
Nad, From Arabidopsis Thaliana
pdb|3K2B|D Chain D, Crystal Structure Of Photosynthetic A4 Isoform
Glyceraldehyde-3- Phosphate Dehydrogenase Complexed With
Nad, From Arabidopsis Thaliana
pdb|3K2B|E Chain E, Crystal Structure Of Photosynthetic A4 Isoform
Glyceraldehyde-3- Phosphate Dehydrogenase Complexed With
Nad, From Arabidopsis Thaliana
pdb|3K2B|F Chain F, Crystal Structure Of Photosynthetic A4 Isoform
Glyceraldehyde-3- Phosphate Dehydrogenase Complexed With
Nad, From Arabidopsis Thaliana
pdb|3K2B|G Chain G, Crystal Structure Of Photosynthetic A4 Isoform
Glyceraldehyde-3- Phosphate Dehydrogenase Complexed With
Nad, From Arabidopsis Thaliana
pdb|3K2B|H Chain H, Crystal Structure Of Photosynthetic A4 Isoform
Glyceraldehyde-3- Phosphate Dehydrogenase Complexed With
Nad, From Arabidopsis Thaliana
pdb|3K2B|O Chain O, Crystal Structure Of Photosynthetic A4 Isoform
Glyceraldehyde-3- Phosphate Dehydrogenase Complexed With
Nad, From Arabidopsis Thaliana
pdb|3K2B|Q Chain Q, Crystal Structure Of Photosynthetic A4 Isoform
Glyceraldehyde-3- Phosphate Dehydrogenase Complexed With
Nad, From Arabidopsis Thaliana
pdb|3QV1|A Chain A, Crystal Structure Of The Binary Complex Of Photosyntetic
A4 Glyceraldehyde 3-Phosphate Dehydrogenase (Gapdh) With
Cp12-2, Both From Arabidopsis Thaliana.
pdb|3QV1|B Chain B, Crystal Structure Of The Binary Complex Of Photosyntetic
A4 Glyceraldehyde 3-Phosphate Dehydrogenase (Gapdh) With
Cp12-2, Both From Arabidopsis Thaliana.
pdb|3QV1|C Chain C, Crystal Structure Of The Binary Complex Of Photosyntetic
A4 Glyceraldehyde 3-Phosphate Dehydrogenase (Gapdh) With
Cp12-2, Both From Arabidopsis Thaliana.
pdb|3QV1|D Chain D, Crystal Structure Of The Binary Complex Of Photosyntetic
A4 Glyceraldehyde 3-Phosphate Dehydrogenase (Gapdh) With
Cp12-2, Both From Arabidopsis Thaliana.
pdb|3QV1|E Chain E, Crystal Structure Of The Binary Complex Of Photosyntetic
A4 Glyceraldehyde 3-Phosphate Dehydrogenase (Gapdh) With
Cp12-2, Both From Arabidopsis Thaliana.
pdb|3QV1|F Chain F, Crystal Structure Of The Binary Complex Of Photosyntetic
A4 Glyceraldehyde 3-Phosphate Dehydrogenase (Gapdh) With
Cp12-2, Both From Arabidopsis Thaliana.
pdb|3RVD|A Chain A, Crystal Structure Of The Binary Complex, Obtained By
Soaking, Of Photosyntetic A4 Glyceraldehyde 3-Phosphate
Dehydrogenase (Gapdh) With Cp12-2, Both From Arabidopsis
Thaliana.
pdb|3RVD|B Chain B, Crystal Structure Of The Binary Complex, Obtained By
Soaking, Of Photosyntetic A4 Glyceraldehyde 3-Phosphate
Dehydrogenase (Gapdh) With Cp12-2, Both From Arabidopsis
Thaliana.
pdb|3RVD|C Chain C, Crystal Structure Of The Binary Complex, Obtained By
Soaking, Of Photosyntetic A4 Glyceraldehyde 3-Phosphate
Dehydrogenase (Gapdh) With Cp12-2, Both From Arabidopsis
Thaliana.
pdb|3RVD|D Chain D, Crystal Structure Of The Binary Complex, Obtained By
Soaking, Of Photosyntetic A4 Glyceraldehyde 3-Phosphate
Dehydrogenase (Gapdh) With Cp12-2, Both From Arabidopsis
Thaliana.
pdb|3RVD|E Chain E, Crystal Structure Of The Binary Complex, Obtained By
Soaking, Of Photosyntetic A4 Glyceraldehyde 3-Phosphate
Dehydrogenase (Gapdh) With Cp12-2, Both From Arabidopsis
Thaliana.
pdb|3RVD|F Chain F, Crystal Structure Of The Binary Complex, Obtained By
Soaking, Of Photosyntetic A4 Glyceraldehyde 3-Phosphate
Dehydrogenase (Gapdh) With Cp12-2, Both From Arabidopsis
Thaliana.
pdb|3RVD|G Chain G, Crystal Structure Of The Binary Complex, Obtained By
Soaking, Of Photosyntetic A4 Glyceraldehyde 3-Phosphate
Dehydrogenase (Gapdh) With Cp12-2, Both From Arabidopsis
Thaliana.
pdb|3RVD|H Chain H, Crystal Structure Of The Binary Complex, Obtained By
Soaking, Of Photosyntetic A4 Glyceraldehyde 3-Phosphate
Dehydrogenase (Gapdh) With Cp12-2, Both From Arabidopsis
Thaliana.
pdb|3RVD|O Chain O, Crystal Structure Of The Binary Complex, Obtained By
Soaking, Of Photosyntetic A4 Glyceraldehyde 3-Phosphate
Dehydrogenase (Gapdh) With Cp12-2, Both From Arabidopsis
Thaliana.
pdb|3RVD|Q Chain Q, Crystal Structure Of The Binary Complex, Obtained By
Soaking, Of Photosyntetic A4 Glyceraldehyde 3-Phosphate
Dehydrogenase (Gapdh) With Cp12-2, Both From Arabidopsis
Thaliana
Length = 337
Score = 32.3 bits (72), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 11/86 (12%)
Query: 244 DLVEMPLLVYVSREKSPEHLHHFKGGALNVLLRVSGVISNSPYILGLDCDMYCNDPTSAR 303
D+V V+V RE + +H+ + GA V++ G Y++G++ D Y +D
Sbjct: 94 DIVIEGTGVFVDREGAGKHI---EAGAKKVIITAPGKGDIPTYVVGVNADAYSHDEPIIS 150
Query: 304 QAMCFHLDPKTSSSLA-FVQ-FPQKF 327
A C T++ LA FV+ QKF
Sbjct: 151 NASC------TTNCLAPFVKVLDQKF 170
>pdb|2WE3|A Chain A, Ebv Dutpase Inactive Mutant Deleted Of Motif V
Length = 264
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 13/52 (25%)
Query: 470 RPQFLGTSTTNLNDVLIQGTRWASGLIDVSIS-------------RFCPLLY 508
RP G S + +L++ RW G +DVS++ RFC L+Y
Sbjct: 173 RPTIFGRSGLAMQGILVKPCRWRRGGVDVSLTNFSDQTVFLNKYRRFCQLVY 224
>pdb|1UF2|K Chain K, The Atomic Structure Of Rice Dwarf Virus (Rdv)
Length = 506
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 172 PQAYFSEAESDENFGDSEFVTEKRKIKEKYE-MFEEQVMKAVEDGEYGN 219
P + +E+E + SE KR + YE ++ E + K V DG YGN
Sbjct: 282 PAVFINESEPFSDKERSELSELKRTDSDAYEKLYSETISKHVSDGSYGN 330
>pdb|2BSY|A Chain A, Epstein Barr Virus Dutpase
pdb|2BT1|A Chain A, Epstein Barr Virus Dutpase In Complex With A,B-Imino Dutp
Length = 278
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 13/52 (25%)
Query: 470 RPQFLGTSTTNLNDVLIQGTRWASGLIDVSIS-------------RFCPLLY 508
RP G S + +L++ RW G +DVS++ RFC L+Y
Sbjct: 165 RPTIFGRSGLAMQGILVKPCRWRRGGVDVSLTNFSDQTVFLNKYRRFCQLVY 216
>pdb|2WE2|A Chain A, Ebv Dutpase Double Mutant Gly78asp-Asp131ser With Dump
Length = 286
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 13/52 (25%)
Query: 470 RPQFLGTSTTNLNDVLIQGTRWASGLIDVSIS-------------RFCPLLY 508
RP G S + +L++ RW G +DVS++ RFC L+Y
Sbjct: 173 RPTIFGRSGLAMQGILVKPCRWRRGGVDVSLTNFSDQTVFLNKYRRFCQLVY 224
>pdb|2WE1|A Chain A, Ebv Dutpase Mutant Asp131asn With Bound Dump
Length = 286
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 13/52 (25%)
Query: 470 RPQFLGTSTTNLNDVLIQGTRWASGLIDVSIS-------------RFCPLLY 508
RP G S + +L++ RW G +DVS++ RFC L+Y
Sbjct: 173 RPTIFGRSGLAMQGILVKPCRWRRGGVDVSLTNFSDQTVFLNKYRRFCQLVY 224
>pdb|2WE0|A Chain A, Ebv Dutpase Mutant Cys4ser
Length = 286
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 13/52 (25%)
Query: 470 RPQFLGTSTTNLNDVLIQGTRWASGLIDVSIS-------------RFCPLLY 508
RP G S + +L++ RW G +DVS++ RFC L+Y
Sbjct: 173 RPTIFGRSGLAMQGILVKPCRWRRGGVDVSLTNFSDQTVFLNKYRRFCQLVY 224
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
0.324 0.139 0.431
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,803,405
Number of Sequences: 62578
Number of extensions: 918517
Number of successful extensions: 2405
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 2396
Number of HSP's gapped (non-prelim): 15
length of query: 745
length of database: 14,973,337
effective HSP length: 106
effective length of query: 639
effective length of database: 8,340,069
effective search space: 5329304091
effective search space used: 5329304091
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 55 (25.8 bits)