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= 017485
(371 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 = 127 bits (318), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 99/374 (26%), Positives = 171/374 (45%), Gaps = 51/374 (13%)
Query: 6 RVLLGIGIGFANQSVPLYLSEMAPPKHRGAFNIGFQVCLAIGVLSANLLNYGTQKI-KGG 64
R++ GIG+G A+ P+Y++E+AP RG Q + G L +NY +
Sbjct: 133 RIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDAS 192
Query: 65 W----GWRISLAMAAAPASILTVGALFMPETPNSIIQRSNDPQKAKRMLQRVRGTADVEA 120
W GWR A PA + + +PE+P ++ R Q A+ +L+++ G
Sbjct: 193 WLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQ-AEGILRKIMGNTLATQ 251
Query: 121 ELNDLIRASSISKTINHPFKKIIQRKYRPQLVM--------AILIPFFQQVTGINIIGLY 172
+ + I +++H RK +L+M +++ FQQ GIN++ Y
Sbjct: 252 AVQE------IKHSLDH------GRKTGGRLLMFGVGVIVIGVMLSIFQQFVGINVVLYY 299
Query: 173 APVLLRTLKXXXXXXXXXXXVVTGGIGTVLTIISMILVDKLGRKILFLVGGIQMFVSQVI 232
AP + +TL +V G I T+++++ VDK GRK L ++G + M +
Sbjct: 300 APEVFKTLGASTDIALLQTIIV-GVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFS 358
Query: 233 IGSIMAAELGDHGGFSEGYAYLILVLVCVYSAGFSYSWGPLAWLVPSEIFPLEIRSAGQS 292
+G+ +++ + L+ + Y A F+ SWGP+ W++ SEIFP IR +
Sbjct: 359 LGTAF---------YTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALA 409
Query: 293 ITVAVCLVFIFFTAQTFLAM------LCHFKAXXXXXXXXWV-----IVMTTFMHLFLPE 341
I VA + +F + TF M + HF W+ ++ FM F+PE
Sbjct: 410 IAVAAQWLANYFVSWTFPMMDKNSWLVAHFH----NGFSYWIYGCMGVLAALFMWKFVPE 465
Query: 342 TKNVPIEQMDKVWR 355
TK +E+++ +W
Sbjct: 466 TKGKTLEELEALWE 479
>pdb|3E80|A Chain A, Structure Of Heparinase Ii Complexed With Heparan Sulfate
Degradation Disaccharide Product
pdb|3E80|B Chain B, Structure Of Heparinase Ii Complexed With Heparan Sulfate
Degradation Disaccharide Product
pdb|3E80|C Chain C, Structure Of Heparinase Ii Complexed With Heparan Sulfate
Degradation Disaccharide Product
Length = 749
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 46/103 (44%), Gaps = 13/103 (12%)
Query: 62 KGGWGWRISLAMAAAPASILTVGALFMPETPNSIIQRSNDPQKAKRMLQRVRGTADVEAE 121
+G W I+ AAA L V IQ +++ Q+ ++R+ G V +
Sbjct: 626 RGEWRVEITPKKAAAEDYYLNV------------IQIADNTQQKLHEVKRIDGDKVVGVQ 673
Query: 122 LND-LIRASSISKTINHPFKKIIQRKYRPQLVMAILIPFFQQV 163
L D ++ S S+T++ PF + K + VM L+P QV
Sbjct: 674 LADRIVTFSKTSETVDRPFGFSVVGKGTFKFVMTDLLPGTWQV 716
>pdb|2FUQ|A Chain A, Crystal Structure Of Heparinase Ii
pdb|2FUQ|B Chain B, Crystal Structure Of Heparinase Ii
Length = 747
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 46/103 (44%), Gaps = 13/103 (12%)
Query: 62 KGGWGWRISLAMAAAPASILTVGALFMPETPNSIIQRSNDPQKAKRMLQRVRGTADVEAE 121
+G W I+ AAA L V IQ +++ Q+ ++R+ G V +
Sbjct: 624 RGEWRVEITPKKAAAEDYYLNV------------IQIADNTQQKLHEVKRIDGDKVVGVQ 671
Query: 122 LND-LIRASSISKTINHPFKKIIQRKYRPQLVMAILIPFFQQV 163
L D ++ S S+T++ PF + K + VM L+P QV
Sbjct: 672 LADRIVTFSKTSETVDRPFGFSVVGKGTFKFVMTDLLPGTWQV 714
>pdb|3E7J|A Chain A, Heparinaseii H202a/y257a Double Mutant Complexed With A
Heparan Sulfate Tetrasaccharide Substrate
pdb|3E7J|B Chain B, Heparinaseii H202a/y257a Double Mutant Complexed With A
Heparan Sulfate Tetrasaccharide Substrate
Length = 749
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 46/103 (44%), Gaps = 13/103 (12%)
Query: 62 KGGWGWRISLAMAAAPASILTVGALFMPETPNSIIQRSNDPQKAKRMLQRVRGTADVEAE 121
+G W I+ AAA L V IQ +++ Q+ ++R+ G V +
Sbjct: 626 RGEWRVEITPKKAAAEDYYLNV------------IQIADNTQQKLHEVKRIDGDKVVGVQ 673
Query: 122 LND-LIRASSISKTINHPFKKIIQRKYRPQLVMAILIPFFQQV 163
L D ++ S S+T++ PF + K + VM L+P QV
Sbjct: 674 LADRIVTFSKTSETVDRPFGFSVVGKGTFKFVMTDLLPGTWQV 716
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
0.327 0.142 0.436
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,702,440
Number of Sequences: 62578
Number of extensions: 353807
Number of successful extensions: 805
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 796
Number of HSP's gapped (non-prelim): 9
length of query: 371
length of database: 14,973,337
effective HSP length: 100
effective length of query: 271
effective length of database: 8,715,537
effective search space: 2361910527
effective search space used: 2361910527
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 bits)