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= 047673
(437 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 = 96.3 bits (238), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 119/479 (24%), Positives = 196/479 (40%), Gaps = 89/479 (18%)
Query: 10 IVAASGGLIFGYDIG-ISGGVTSMEPFLKKFFLEVYRKMKEDTKISNYCKFDSQLLAAFT 68
+VA GGL+FGYD ISG V S L F+ + + E + LL
Sbjct: 15 LVATLGGLLFGYDTAVISGTVES----LNTVFVAP-QNLSESAA--------NSLLGFCV 61
Query: 69 SSLYIAGLIASLFASTVTRAFGRKASILVGGTTFLTSSA------IGGAALD-------- 114
+S I +I + FGR+ S+ + F S +G +++
Sbjct: 62 ASALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVY 121
Query: 115 ---------IYMLILGLN-------APISLRNGTPKHIGGFNIGF-QVCVATGILSANLL 157
IY +I G+ +P+ + P HI G + F Q + G L +
Sbjct: 122 LAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCV 181
Query: 158 NYGTQKI-KGGW----GWRISLAMAVAPASILTIGLLFLPETPSSIIQRNNDYQKAEKIM 212
NY + W GWR A PA + + L +PE+P ++ R ++AE I+
Sbjct: 182 NYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQ-EQAEGIL 240
Query: 213 QIVRGTA-------DVQAELDDLIRQSS-------------VSKNINHPFKKI-IDRKYR 251
+ + G +++ LD + V +I F I + Y
Sbjct: 241 RKIMGNTLATQAVQEIKHSLDHGRKTGGRLLMFGVGVIVIGVMLSIFQQFVGINVVLYYA 300
Query: 252 PQL---LSESTSL-LMSALVTGGIGTVSTILPMILADKLGRKVLFLLGGIQILVSQVMIG 307
P++ L ST + L+ ++ G I T+L ++ DK GRK L ++G + + + +G
Sbjct: 301 PEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLG 360
Query: 308 SVMATQ------LVLICVYNAGFTFLWWPLGWLVPSEIFPLEIRSAGKSITVAVGLLFTS 361
+ TQ L+ + Y A F W P+ W++ SEIFP IR +I VA L
Sbjct: 361 TAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANY 420
Query: 362 LVAQTVLAM------LYHFKAGV-FFFFGGWLIAMTTFVHFFLPETKNVPIEQMDKVWR 413
V+ T M + HF G ++ +G + F+ F+PETK +E+++ +W
Sbjct: 421 FVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALWE 479
>pdb|3BZ6|A Chain A, Crystal Structure Of A Conserved Protein Of Unknown
Function From Pseudomonas Syringae Pv. Tomato Str.
Dc3000
Length = 183
Score = 32.7 bits (73), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 10/62 (16%)
Query: 168 WGWRISLAMAVAPASILTIGLLFL--PETPSSIIQRNN---DYQKAEKIMQ-----IVRG 217
W ++ + + PA ++ GLL L P+T S ++ R+N D++ +E+++ I RG
Sbjct: 96 WEHKVDKGLELVPAQVILTGLLLLRGPQTVSELLTRSNRXHDFEDSEQVVHQLERLIARG 155
Query: 218 TA 219
A
Sbjct: 156 LA 157
>pdb|3O8Q|B Chain B, 1.45 Angstrom Resolution Crystal Structure Of Shikimate 5-
Dehydrogenase (Aroe) From Vibrio Cholerae
Length = 275
Score = 29.3 bits (64), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 26/43 (60%)
Query: 190 FLPETPSSIIQRNNDYQKAEKIMQIVRGTADVQAELDDLIRQS 232
L + P+SI N + KAE++ ++V +V+A+ + ++QS
Sbjct: 139 LLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFEQLKQS 181
>pdb|3PGJ|A Chain A, 2.49 Angstrom Resolution Crystal Structure Of Shikimate 5-
Dehydrogenase (Aroe) From Vibrio Cholerae O1 Biovar
Eltor Str. N16961 In Complex With Shikimate
pdb|3PGJ|B Chain B, 2.49 Angstrom Resolution Crystal Structure Of Shikimate 5-
Dehydrogenase (Aroe) From Vibrio Cholerae O1 Biovar
Eltor Str. N16961 In Complex With Shikimate
pdb|3PGJ|C Chain C, 2.49 Angstrom Resolution Crystal Structure Of Shikimate 5-
Dehydrogenase (Aroe) From Vibrio Cholerae O1 Biovar
Eltor Str. N16961 In Complex With Shikimate
pdb|3PGJ|D Chain D, 2.49 Angstrom Resolution Crystal Structure Of Shikimate 5-
Dehydrogenase (Aroe) From Vibrio Cholerae O1 Biovar
Eltor Str. N16961 In Complex With Shikimate
pdb|3SEF|A Chain A, 2.4 Angstrom Resolution Crystal Structure Of Shikimate
5-Dehydrogenase (Aroe) From Vibrio Cholerae O1 Biovar
Eltor Str. N16961 In Complex With Shikimate And Nadph
pdb|3SEF|B Chain B, 2.4 Angstrom Resolution Crystal Structure Of Shikimate
5-Dehydrogenase (Aroe) From Vibrio Cholerae O1 Biovar
Eltor Str. N16961 In Complex With Shikimate And Nadph
pdb|3SEF|C Chain C, 2.4 Angstrom Resolution Crystal Structure Of Shikimate
5-Dehydrogenase (Aroe) From Vibrio Cholerae O1 Biovar
Eltor Str. N16961 In Complex With Shikimate And Nadph
pdb|3SEF|D Chain D, 2.4 Angstrom Resolution Crystal Structure Of Shikimate
5-Dehydrogenase (Aroe) From Vibrio Cholerae O1 Biovar
Eltor Str. N16961 In Complex With Shikimate And Nadph
Length = 302
Score = 29.3 bits (64), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 26/43 (60%)
Query: 190 FLPETPSSIIQRNNDYQKAEKIMQIVRGTADVQAELDDLIRQS 232
L + P+SI N + KAE++ ++V +V+A+ + ++QS
Sbjct: 166 LLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFEQLKQS 208
>pdb|3O8Q|A Chain A, 1.45 Angstrom Resolution Crystal Structure Of Shikimate 5-
Dehydrogenase (Aroe) From Vibrio Cholerae
Length = 281
Score = 29.3 bits (64), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 26/43 (60%)
Query: 190 FLPETPSSIIQRNNDYQKAEKIMQIVRGTADVQAELDDLIRQS 232
L + P+SI N + KAE++ ++V +V+A+ + ++QS
Sbjct: 145 LLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFEQLKQS 187
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
0.325 0.140 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,787,014
Number of Sequences: 62578
Number of extensions: 454240
Number of successful extensions: 1396
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1388
Number of HSP's gapped (non-prelim): 9
length of query: 437
length of database: 14,973,337
effective HSP length: 102
effective length of query: 335
effective length of database: 8,590,381
effective search space: 2877777635
effective search space used: 2877777635
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 bits)