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= 043907
(330 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 = 98.2 bits (243), Expect = 6e-21, Method: Compositional matrix adjust.
Identities = 80/289 (27%), Positives = 138/289 (47%), Gaps = 37/289 (12%)
Query: 34 AFNIYMLIFGRLLL-GVGIGFGNQIKGGW----GWRISLAMAAAPASILTIGAIFLPETP 88
+FN + +IFG+LL+ V W GWR A PA + + +PE+P
Sbjct: 165 SFNQFAIIFGQLLVYCVNYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESP 224
Query: 89 NSKIQRSDDHQKAQKMLQRIRG-------ISDVKAELNDLIRASSTSKSITQPFKNIIQR 141
+ R Q A+ +L++I G + ++K L+ T + +I
Sbjct: 225 RWLMSRGKQEQ-AEGILRKIMGNTLATQAVQEIKHSLD---HGRKTGGRLLMFGVGVI-- 278
Query: 142 KYRPQPVMAILIPFFQQVTGINIVGLYSPVLFRTLKLGESTSL-LLSAVVAGGMGTVLAI 200
V+ +++ FQQ GIN+V Y+P +F+TL G ST + LL ++ G + +
Sbjct: 279 ------VIGVMLSIFQQFVGINVVLYYAPEVFKTL--GASTDIALLQTIIVGVINLTFTV 330
Query: 201 ISMILADKFGRKVLFLVGGMQMLVSQVIIGSIMAAQLGDHGGCSEGYAYLILVLVCLCSS 260
++++ DKFGRK L ++G + M + +G+ Q + G L+ +L + +
Sbjct: 331 LAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYTQ-------APGIVALLSMLFYVAA- 382
Query: 261 GYCYSWGPLAWLVPSEIFPLEIRSAGQSITVAVNFVFTFLTAQTFLPML 309
+ SWGP+ W++ SEIFP IR +I VA ++ + + TF PM+
Sbjct: 383 -FAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTF-PMM 429
>pdb|3I3L|A Chain A, Crystal Structure Of Cmls, A Flavin-Dependent Halogenase
Length = 591
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 13/75 (17%)
Query: 74 ASILTIGAIFLPETPNSKIQRSDDHQKAQKMLQRIRGISDVKAELNDLIRASSTSKSITQ 133
++++ IG PE SDD +A+ R+R ISD+ LN + R T
Sbjct: 433 STMIAIGRHQRPEL-------SDDFSEAELNPARVRWISDLTKRLNSITRFKWTGG---- 481
Query: 134 PFKNIIQRKYRPQPV 148
K ++++ YR +P+
Sbjct: 482 --KAVLKQHYRVEPI 494
>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 = 28.1 bits (61), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 13/79 (16%)
Query: 58 KGGWGWRISLAMAAAPASILTIGAIFLPETPNSKIQRSDDHQKAQKMLQRIRGISDVKAE 117
+G W I+ AAA L + IQ +D+ Q+ ++RI G V +
Sbjct: 626 RGEWRVEITPKKAAAEDYYLNV------------IQIADNTQQKLHEVKRIDGDKVVGVQ 673
Query: 118 LND-LIRASSTSKSITQPF 135
L D ++ S TS+++ +PF
Sbjct: 674 LADRIVTFSKTSETVDRPF 692
>pdb|2FUQ|A Chain A, Crystal Structure Of Heparinase Ii
pdb|2FUQ|B Chain B, Crystal Structure Of Heparinase Ii
Length = 747
Score = 28.1 bits (61), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 13/79 (16%)
Query: 58 KGGWGWRISLAMAAAPASILTIGAIFLPETPNSKIQRSDDHQKAQKMLQRIRGISDVKAE 117
+G W I+ AAA L + IQ +D+ Q+ ++RI G V +
Sbjct: 624 RGEWRVEITPKKAAAEDYYLNV------------IQIADNTQQKLHEVKRIDGDKVVGVQ 671
Query: 118 LND-LIRASSTSKSITQPF 135
L D ++ S TS+++ +PF
Sbjct: 672 LADRIVTFSKTSETVDRPF 690
>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 = 28.1 bits (61), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 13/79 (16%)
Query: 58 KGGWGWRISLAMAAAPASILTIGAIFLPETPNSKIQRSDDHQKAQKMLQRIRGISDVKAE 117
+G W I+ AAA L + IQ +D+ Q+ ++RI G V +
Sbjct: 626 RGEWRVEITPKKAAAEDYYLNV------------IQIADNTQQKLHEVKRIDGDKVVGVQ 673
Query: 118 LND-LIRASSTSKSITQPF 135
L D ++ S TS+++ +PF
Sbjct: 674 LADRIVTFSKTSETVDRPF 692
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
0.326 0.141 0.415
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,152,251
Number of Sequences: 62578
Number of extensions: 309593
Number of successful extensions: 902
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 895
Number of HSP's gapped (non-prelim): 7
length of query: 330
length of database: 14,973,337
effective HSP length: 99
effective length of query: 231
effective length of database: 8,778,115
effective search space: 2027744565
effective search space used: 2027744565
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)