BLASTP 2.2.1 [Apr-13-2001]
Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
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.
Query= gi|15645865|ref|NP_208043.1| oligopeptide ABC
transporter, permease protein (oppB) [Helicobacter pylori 26695]
(348 letters)
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
13,198 sequences; 2,899,336 total letters
Searching...........................done
Score E
Sequences producing significant alignments: (bits) Value
pdb|1JR3|A Chain A, Crystal Structure Of The Processivity C... 32 0.11
pdb|1KDV|A Chain A, Pseudomonas Serine-Carboxyl Proteinase ... 29 0.69
pdb|1GA1|A Chain A, Crystal Structure Analysis Of Pscp (Pse... 29 0.69
pdb|1JB0|B Chain B, Crystal Structure Of Photosystem I: A P... 27 2.6
pdb|1LN1|A Chain A, Crystal Structure Of Human Phosphatidyl... 27 3.4
pdb|1LN2|A Chain A, Crystal Structure Of Human Phosphatidyl... 27 4.5
pdb|1M2O|A Chain A, Crystal Structure Of The Sec23-Sar1 Com... 26 5.9
pdb|1G29|1 Chain 1, Malk >gi|12084695|pdb|1G29|2 Chain 2, Malk 26 5.9
>pdb|1JR3|A Chain A, Crystal Structure Of The Processivity Clamp Loader Gamma
Complex Of E. Coli Dna Polymerase Iii
pdb|1JR3|C Chain C, Crystal Structure Of The Processivity Clamp Loader Gamma
Complex Of E. Coli Dna Polymerase Iii
pdb|1JR3|B Chain B, Crystal Structure Of The Processivity Clamp Loader Gamma
Complex Of E. Coli Dna Polymerase Iii
Length = 373
Score = 32.0 bits (71), Expect = 0.11
Identities = 14/30 (46%), Positives = 23/30 (76%)
Query: 234 SFLDEMGKLYVLSAKAKGCSVGRIFYAHVF 263
+F D +G+ +VL+A A G S+GRI +A++F
Sbjct: 14 TFADVVGQEHVLTALANGLSLGRIHHAYLF 43
>pdb|1KDV|A Chain A, Pseudomonas Serine-Carboxyl Proteinase Complexed With The
Inhibitor Aiaf
pdb|1KDY|A Chain A, Pseudomonas Serine-Carboxyl Proteinase Complexed With The
Inhibitor Aipf
pdb|1KDZ|A Chain A, Pseudomonas Serine-Carboxyl Proteinase Complexed With The
Inhibitor Tyrostatin
pdb|1KE1|A Chain A, Pseudomonas Serine-Carboxyl Proteinase Complexed With The
Inhibitor Pseudotyrostatin
pdb|1KE2|A Chain A, Pseudomonas Serine-Carboxyl Proteinase Complexed With The
Inhibitor Chymostatin
Length = 370
Score = 29.3 bits (64), Expect = 0.69
Identities = 21/59 (35%), Positives = 28/59 (46%), Gaps = 2/59 (3%)
Query: 273 GFPQAFLGMFFSS--SLLIEIVFSLDGLGLLGYESIVSRDYPVVFGSLYIFTLLGLVAS 329
GFP A SS SL+ ++ +G G GY + DYP +GSL I L + S
Sbjct: 309 GFPAASFYSAISSTPSLVHDVKSGNNGYGGYGYNAGTGWDYPTGWGSLDIAKLSAYIRS 367
>pdb|1GA1|A Chain A, Crystal Structure Analysis Of Pscp (Pseudomonas Serine-
Carboxyl Proteinase) Complexed With A Fragment Of
Iodotyrostatin
pdb|1GA6|A Chain A, Crystal Structure Analysis Of Pscp (Pseudomonas Serine-
Carboxyl Proteinase) Complexed With A Fragment Of
Tyrostati
pdb|1GA4|A Chain A, Crystal Structure Analysis Of Pscp (Pseudomonas Serine-
Carboxyl Proteinase) Complexed With Inhibitor
Pseudoiodotyrostatin
Length = 372
Score = 29.3 bits (64), Expect = 0.69
Identities = 21/59 (35%), Positives = 28/59 (46%), Gaps = 2/59 (3%)
Query: 273 GFPQAFLGMFFSS--SLLIEIVFSLDGLGLLGYESIVSRDYPVVFGSLYIFTLLGLVAS 329
GFP A SS SL+ ++ +G G GY + DYP +GSL I L + S
Sbjct: 309 GFPAASFYSAISSTPSLVHDVKSGNNGYGGYGYNAGTGWDYPTGWGSLDIAKLSAYIRS 367
>pdb|1JB0|B Chain B, Crystal Structure Of Photosystem I: A Photosynthetic
Reaction Center And Core Antenna System From
Cyanobacteria
Length = 740
Score = 27.3 bits (59), Expect = 2.6
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 182 YWHWFPL---KGLVSD-NFESLSALGKIKDYLW 210
YWHW L +G V+ N S +G ++DYLW
Sbjct: 599 YWHWKHLGVWEGNVAQFNESSTYLMGWLRDYLW 631
>pdb|1LN1|A Chain A, Crystal Structure Of Human Phosphatidylcholine Transfer
Protein In Complex With Dilinoleoylphosphatidylcholine
Length = 214
Score = 26.9 bits (58), Expect = 3.4
Identities = 15/41 (36%), Positives = 23/41 (55%), Gaps = 1/41 (2%)
Query: 46 QSKEIQGVVKERSYRASQGLESDLLENLKK-LYGFDKPIGE 85
Q E GV++ + Y+ S +ESD + K +Y FD P G+
Sbjct: 142 QLGERSGVIRVKQYKQSLAIESDGKKGSKVFMYYFDNPGGQ 182
>pdb|1LN2|A Chain A, Crystal Structure Of Human Phosphatidylcholine Transfer
Protein In Complex With Dilinoleoylphosphatidylcholine
(Seleno-Met Protein)
pdb|1LN2|B Chain B, Crystal Structure Of Human Phosphatidylcholine Transfer
Protein In Complex With Dilinoleoylphosphatidylcholine
(Seleno-Met Protein)
pdb|1LN3|A Chain A, Structure Of Human Phosphatidylcholine Transfer Protein In
Complex With Palmitoyl-Linoleoyl Phosphatidylcholine
(Seleno-Met Protein)
pdb|1LN3|B Chain B, Structure Of Human Phosphatidylcholine Transfer Protein In
Complex With Palmitoyl-Linoleoyl Phosphatidylcholine
(Seleno-Met Protein)
Length = 214
Score = 26.6 bits (57), Expect = 4.5
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 32 GGPIEQMMAKINNT-QSKEIQGVVKERSYRASQGLESDLLENLKKL-YGFDKPIGE 85
G I ++A+ + Q E GV++ + Y+ S +ESD + K Y FD P G+
Sbjct: 127 GRKIHVILARSTSXPQLGERSGVIRVKQYKQSLAIESDGKKGSKVFXYYFDNPGGQ 182
>pdb|1M2O|A Chain A, Crystal Structure Of The Sec23-Sar1 Complex
pdb|1M2O|C Chain C, Crystal Structure Of The Sec23-Sar1 Complex
pdb|1M2V|A Chain A, Crystal Structure Of The Yeast Sec2324 HETERODIMER
Length = 768
Score = 26.2 bits (56), Expect = 5.9
Identities = 13/52 (25%), Positives = 27/52 (51%)
Query: 258 FYAHVFRNAILLVVAGFPQAFLGMFFSSSLLIEIVFSLDGLGLLGYESIVSR 309
F +F+ + L + A + +L M F+ ++ ++ L GL+G+ S V +
Sbjct: 375 FSTAIFKQSYLRLFAKDEEGYLKMAFNGNMAVKTSKDLKVQGLIGHASAVKK 426
>pdb|1G29|1 Chain 1, Malk
pdb|1G29|2 Chain 2, Malk
Length = 372
Score = 26.2 bits (56), Expect = 5.9
Identities = 10/26 (38%), Positives = 19/26 (72%)
Query: 60 RASQGLESDLLENLKKLYGFDKPIGE 85
R +G+E D++ ++KK++ FDK G+
Sbjct: 344 RVREGVEVDVVFDMKKIHIFDKTTGK 369
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
Posted date: Dec 20, 2002 11:08 AM
Number of letters in database: 2,899,336
Number of sequences in database: 13,198
Lambda K H
0.328 0.146 0.424
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,798,138
Number of Sequences: 13198
Number of extensions: 71529
Number of successful extensions: 149
Number of sequences better than 10.0: 8
Number of HSP's better than 10.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 144
Number of HSP's gapped (non-prelim): 8
length of query: 348
length of database: 2,899,336
effective HSP length: 89
effective length of query: 259
effective length of database: 1,724,714
effective search space: 446700926
effective search space used: 446700926
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: 55 (25.8 bits)