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= psy7965
(257 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GBY|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To D-Xylose
pdb|4GBZ|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To D-Glucose
pdb|4GC0|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To
6-Bromo-6-Deoxy-D-Glucose
Length = 491
Score = 84.0 bits (206), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 73/275 (26%), Positives = 126/275 (45%), Gaps = 62/275 (22%)
Query: 37 VARFIAGVGTGGLCAIIPMFIGEIAESSIRGALGSFFQMFLTLGVLYVYCLG-------- 88
+ R I G+G G + PM+I E+A + IRG L SF Q + G L VYC+
Sbjct: 131 IYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGD 190
Query: 89 ---LST---YTVIAIGCL--------------TPIFLMKSGKPEKAEVSLRYYRGAQYDV 128
L+T + A C+ +P +LM GK E+AE LR G +
Sbjct: 191 ASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGN--TL 248
Query: 129 ATELAAIQKEIDAASEKKATFSDLFSSRANLRGLIVSLGLMIFQQFSGVNTVIFYSNDIF 188
AT+ A+Q+ + + T L + +++ + L IFQQF G+N V++Y+ ++F
Sbjct: 249 ATQ--AVQEIKHSLDHGRKTGGRLLMFGVGV--IVIGVMLSIFQQFVGINVVLYYAPEVF 304
Query: 189 KSAGSTLDPS-ISAIIVGVVQCIVTGLSNSGSD--------------------------- 220
K+ G++ D + + IIVGV+ T L+ D
Sbjct: 305 KTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFY 364
Query: 221 VSSIAFLPLISVIMFIVMFSLGFGPIPWMMVGELF 255
+ + L+S++ ++ F++ +GP+ W+++ E+F
Sbjct: 365 TQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIF 399
>pdb|2IX8|A Chain A, Model For Eef3 Bound To An 80s Ribosome
Length = 976
Score = 30.8 bits (68), Expect = 0.78, Method: Composition-based stats.
Identities = 15/41 (36%), Positives = 22/41 (53%)
Query: 193 STLDPSISAIIVGVVQCIVTGLSNSGSDVSSIAFLPLISVI 233
S L PS+ IV +V I T N ++ S+A LIS++
Sbjct: 77 SNLSPSVEPYIVQLVPAICTNAGNKDKEIQSVASETLISIV 117
>pdb|2IWH|A Chain A, Structure Of Yeast Elongation Factor 3 In Complex With
Adpnp
pdb|2IWH|B Chain B, Structure Of Yeast Elongation Factor 3 In Complex With
Adpnp
pdb|2IX3|A Chain A, Structure Of Yeast Elongation Factor 3
pdb|2IX3|B Chain B, Structure Of Yeast Elongation Factor 3
Length = 986
Score = 30.8 bits (68), Expect = 0.78, Method: Composition-based stats.
Identities = 15/41 (36%), Positives = 22/41 (53%)
Query: 193 STLDPSISAIIVGVVQCIVTGLSNSGSDVSSIAFLPLISVI 233
S L PS+ IV +V I T N ++ S+A LIS++
Sbjct: 83 SNLSPSVEPYIVQLVPAICTNAGNKDKEIQSVASETLISIV 123
>pdb|2IW3|A Chain A, Elongation Factor 3 In Complex With Adp
pdb|2IW3|B Chain B, Elongation Factor 3 In Complex With Adp
Length = 986
Score = 30.8 bits (68), Expect = 0.78, Method: Composition-based stats.
Identities = 15/41 (36%), Positives = 22/41 (53%)
Query: 193 STLDPSISAIIVGVVQCIVTGLSNSGSDVSSIAFLPLISVI 233
S L PS+ IV +V I T N ++ S+A LIS++
Sbjct: 83 SNLSPSVEPYIVQLVPAICTNAGNKDKEIQSVASETLISIV 123
>pdb|4AQ4|A Chain A, Substrate Bound Sn-Glycerol-3-Phosphate Binding
Periplasmic Protein Ugpb From Escherichia Coli
Length = 419
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 167 GLMIFQQFSGVNTVIFYSNDIFKSAGSTLDPS 198
G ++ Q F+ V++Y+ D FK AG LDP
Sbjct: 115 GHLLSQPFNSSTPVLYYNKDAFKKAG--LDPE 144
>pdb|2XUT|A Chain A, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
Family Transporter.
pdb|2XUT|B Chain B, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
Family Transporter.
pdb|2XUT|C Chain C, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
Family Transporter
Length = 524
Score = 27.3 bits (59), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 2/76 (2%)
Query: 3 ADKF-GRKPVILAFCFPYILSW-LLILFAQNIYMLFVARFIAGVGTGGLCAIIPMFIGEI 60
AD+F G+ IL Y + L +F ++ + F+ +G+GG+ ++ F+G+
Sbjct: 78 ADRFFGKYNTILWLSLIYCVGHAFLAIFEHSVQGFYTGLFLIALGSGGIKPLVSSFMGDQ 137
Query: 61 AESSIRGALGSFFQMF 76
+ S + F MF
Sbjct: 138 FDQSNKSLAQKAFDMF 153
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
0.329 0.143 0.425
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,568,645
Number of Sequences: 62578
Number of extensions: 242791
Number of successful extensions: 631
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 621
Number of HSP's gapped (non-prelim): 17
length of query: 257
length of database: 14,973,337
effective HSP length: 97
effective length of query: 160
effective length of database: 8,903,271
effective search space: 1424523360
effective search space used: 1424523360
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 bits)