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= 047275
(319 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 = 77.0 bits (188), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 59/222 (26%), Positives = 106/222 (47%), Gaps = 33/222 (14%)
Query: 110 PLYLSEMAPPKHRG---AFNIGFQVCTAIGVLGANLLNYGTQKI-KGGW----GWRISLS 161
P+Y++E+AP RG +FN Q G L +NY + W GWR +
Sbjct: 148 PMYIAELAPAHIRGKLVSFN---QFAIIFGQLLVYCVNYFIARSGDASWLNTDGWRYMFA 204
Query: 162 MAAAPASILTLGALILPDTPNSIIQRSNGHEKAKKMLQRVRGTADVQAELDDLIRASIVS 221
PA + + +P++P ++ R E+A+ +L+++ G A+
Sbjct: 205 SECIPALLFLMLLYTVPESPRWLMSRGK-QEQAEGILRKIMGNT----------LATQAV 253
Query: 222 RTVKHPFQTIIQRKYRPQLVM--------AILIPFFQQLTGINVISFYAPVLFRTIKLSE 273
+ +KH RK +L+M +++ FQQ GINV+ +YAP +F+T+ S
Sbjct: 254 QEIKHSLDH--GRKTGGRLLMFGVGVIVIGVMLSIFQQFVGINVVLYYAPEVFKTLGAST 311
Query: 274 STSLLMSAVVTGGVSTIATITSMILTDKLGRKVLFLVGGILM 315
+LL + ++ G ++ T+ +++ DK GRK L ++G + M
Sbjct: 312 DIALLQT-IIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGM 352
>pdb|4FO4|A Chain A, Inosine 5'-Monophosphate Dehydrogenase From Vibrio
Cholerae, Deletion Mutant, Complexed With Imp And
Mycophenolic Acid
pdb|4FO4|B Chain B, Inosine 5'-Monophosphate Dehydrogenase From Vibrio
Cholerae, Deletion Mutant, Complexed With Imp And
Mycophenolic Acid
pdb|4HLV|A Chain A, Inosine 5'-Monophosphate Dehydrogenase From Vibrio
Cholerae, Deletion Mutant, In Complex With Nad And Imp
pdb|4HLV|B Chain B, Inosine 5'-Monophosphate Dehydrogenase From Vibrio
Cholerae, Deletion Mutant, In Complex With Nad And Imp
pdb|4IX2|A Chain A, Inosine 5'-monophosphate Dehydrogenase From Vibrio
Cholerae, Deletion Mutant, Complexed With Imp
pdb|4IX2|B Chain B, Inosine 5'-monophosphate Dehydrogenase From Vibrio
Cholerae, Deletion Mutant, Complexed With Imp
pdb|4IX2|C Chain C, Inosine 5'-monophosphate Dehydrogenase From Vibrio
Cholerae, Deletion Mutant, Complexed With Imp
pdb|4IX2|D Chain D, Inosine 5'-monophosphate Dehydrogenase From Vibrio
Cholerae, Deletion Mutant, Complexed With Imp
Length = 366
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 148 QKIKGGWGWRISLSMAAAPASILTLGALILPDTPNSIIQRSNGHEKAKKMLQRVRGT 204
++K G R+ ++ AAP + + AL+ +I S+GH + +LQR+R T
Sbjct: 89 HQVKISGGLRVGAAVGAAPGNEERVKALVEAGVDVLLIDSSHGHSEG--VLQRIRET 143
>pdb|2O7P|A Chain A, The Crystal Structure Of Ribd From Escherichia Coli In
Complex With The Oxidised Nadp+ Cofactor In The Active
Site Of The Reductase Domain
pdb|2O7P|B Chain B, The Crystal Structure Of Ribd From Escherichia Coli In
Complex With The Oxidised Nadp+ Cofactor In The Active
Site Of The Reductase Domain
Length = 380
Score = 28.5 bits (62), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 39/85 (45%), Gaps = 5/85 (5%)
Query: 168 SILTLGALILPDTPNSIIQRSNGHEKAKKMLQRVRGTADVQAELDDLIRASIVSRTVKHP 227
+ILT A +L D P ++ S E+ + + + ++ +D R + V R V+ P
Sbjct: 194 AILTSSATVLADDPALTVRWSELDEQTQALYPQQNLRQPIRIVIDSQNRVTPVHRIVQQP 253
Query: 228 FQTIIQR-----KYRPQLVMAILIP 247
+T R + P+ V +LIP
Sbjct: 254 GETWFARTQEDSREWPETVRTLLIP 278
>pdb|2G6V|A Chain A, The Crystal Structure Of Ribd From Escherichia Coli
pdb|2G6V|B Chain B, The Crystal Structure Of Ribd From Escherichia Coli
pdb|2OBC|A Chain A, The Crystal Structure Of Ribd From Escherichia Coli In
Complex With A Substrate Analogue, Ribose 5-Phosphate
(Beta Form), Bound To The Active Site Of The Reductase
Domain
pdb|2OBC|B Chain B, The Crystal Structure Of Ribd From Escherichia Coli In
Complex With A Substrate Analogue, Ribose 5-Phosphate
(Beta Form), Bound To The Active Site Of The Reductase
Domain
Length = 402
Score = 28.5 bits (62), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 41/91 (45%), Gaps = 5/91 (5%)
Query: 162 MAAAPASILTLGALILPDTPNSIIQRSNGHEKAKKMLQRVRGTADVQAELDDLIRASIVS 221
+ A +ILT A +L D P ++ S E+ + + + ++ +D R + V
Sbjct: 210 LRAQSHAILTSSATVLADDPALTVRWSELDEQTQALYPQQNLRQPIRIVIDSQNRVTPVH 269
Query: 222 RTVKHPFQTIIQR-----KYRPQLVMAILIP 247
R V+ P +T R + P+ V +LIP
Sbjct: 270 RIVQQPGETWFARTQEDSREWPETVRTLLIP 300
>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 = 6.3, Method: Compositional matrix adjust.
Identities = 29/115 (25%), Positives = 48/115 (41%), Gaps = 14/115 (12%)
Query: 137 VLGANLLNY---GTQKIKGGWGWRISLSMAAAPASILTLGALILPDTPNSIIQRSNGHEK 193
V G N N GT + WR+ ++ A A L ++IQ ++ ++
Sbjct: 607 VFGTNYTNDPKPGTDEALERGEWRVEITPKKAAAEDYYL----------NVIQIADNTQQ 656
Query: 194 AKKMLQRVRGTADVQAEL-DDLIRASIVSRTVKHPFQTIIQRKYRPQLVMAILIP 247
++R+ G V +L D ++ S S TV PF + K + VM L+P
Sbjct: 657 KLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVVGKGTFKFVMTDLLP 711
>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 = 6.7, Method: Compositional matrix adjust.
Identities = 29/115 (25%), Positives = 48/115 (41%), Gaps = 14/115 (12%)
Query: 137 VLGANLLNY---GTQKIKGGWGWRISLSMAAAPASILTLGALILPDTPNSIIQRSNGHEK 193
V G N N GT + WR+ ++ A A L ++IQ ++ ++
Sbjct: 605 VFGTNYTNDPKPGTDEALERGEWRVEITPKKAAAEDYYL----------NVIQIADNTQQ 654
Query: 194 AKKMLQRVRGTADVQAEL-DDLIRASIVSRTVKHPFQTIIQRKYRPQLVMAILIP 247
++R+ G V +L D ++ S S TV PF + K + VM L+P
Sbjct: 655 KLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVVGKGTFKFVMTDLLP 709
>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 = 6.8, Method: Compositional matrix adjust.
Identities = 29/115 (25%), Positives = 48/115 (41%), Gaps = 14/115 (12%)
Query: 137 VLGANLLNY---GTQKIKGGWGWRISLSMAAAPASILTLGALILPDTPNSIIQRSNGHEK 193
V G N N GT + WR+ ++ A A L ++IQ ++ ++
Sbjct: 607 VFGTNYTNDPKPGTDEALERGEWRVEITPKKAAAEDYYL----------NVIQIADNTQQ 656
Query: 194 AKKMLQRVRGTADVQAEL-DDLIRASIVSRTVKHPFQTIIQRKYRPQLVMAILIP 247
++R+ G V +L D ++ S S TV PF + K + VM L+P
Sbjct: 657 KLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVVGKGTFKFVMTDLLP 711
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
0.323 0.136 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,889,324
Number of Sequences: 62578
Number of extensions: 220398
Number of successful extensions: 435
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 432
Number of HSP's gapped (non-prelim): 11
length of query: 319
length of database: 14,973,337
effective HSP length: 99
effective length of query: 220
effective length of database: 8,778,115
effective search space: 1931185300
effective search space used: 1931185300
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 bits)