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|15645006|ref|NP_207176.1| cytochrome c biogenesis
protein (ycf5) [Helicobacter pylori 26695]
(936 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|1K4Z|A Chain A, C-Terminal Domain Of Cyclase Associated... 29 2.1
pdb|1KQ5|A Chain A, C-Terminal Domain Of Cyclase Associated... 29 2.1
pdb|1E12|A Chain A, Halorhodopsin, A Light-Driven Chloride ... 28 3.6
pdb|1PRG|A Chain A, Ligand Binding Domain Of The Human Pero... 28 4.7
pdb|3PRG|A Chain A, Ligand Binding Domain Of Human Peroxiso... 28 4.7
pdb|1K74|D Chain D, The 2.3 Angstrom Resolution Crystal Str... 28 4.7
pdb|2PRG|A Chain A, Ligand-Binding Domain Of The Human Pero... 28 4.7
pdb|1FM6|D Chain D, The 2.1 Angstrom Resolution Crystal Str... 28 4.7
pdb|1I7I|A Chain A, Crystal Structure Of The Ligand Binding... 28 4.7
pdb|1QHL|A Chain A, Crystal Structure Of The N-Terminal Dom... 27 8.0
>pdb|1K4Z|A Chain A, C-Terminal Domain Of Cyclase Associated Protein
pdb|1K4Z|B Chain B, C-Terminal Domain Of Cyclase Associated Protein
Length = 159
Score = 29.3 bits (64), Expect = 2.1
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 558 IEAISSPNKEISSVATEFLKNIFSGFDDALKTNQWD-KVEKTLKDLSIYQKEHAKNLYLS 616
+ AIS E SV L + SG D +K+N++ +V +L +SI K N+YLS
Sbjct: 50 VNAISLSETESCSVV---LDSSISGMD-VIKSNKFGIQVNHSLPQISI-DKSDGGNIYLS 104
Query: 617 SSKVDSEIFLNHTNFFN 633
+++EI+ + + N
Sbjct: 105 KESLNTEIYTSCSTAIN 121
>pdb|1KQ5|A Chain A, C-Terminal Domain Of Cyclase Associated Protein With Pro
505 Replaced By Ser (P505s)
pdb|1KQ5|B Chain B, C-Terminal Domain Of Cyclase Associated Protein With Pro
505 Replaced By Ser (P505s)
Length = 159
Score = 29.3 bits (64), Expect = 2.1
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 558 IEAISSPNKEISSVATEFLKNIFSGFDDALKTNQWD-KVEKTLKDLSIYQKEHAKNLYLS 616
+ AIS E SV L + SG D +K+N++ +V +L +SI K N+YLS
Sbjct: 50 VNAISLSETESCSVV---LDSSISGMD-VIKSNKFGIQVNHSLPQISI-DKSDGGNIYLS 104
Query: 617 SSKVDSEIFLNHTNFFN 633
+++EI+ + + N
Sbjct: 105 KESLNTEIYTSCSTAIN 121
>pdb|1E12|A Chain A, Halorhodopsin, A Light-Driven Chloride Pump
Length = 253
Score = 28.5 bits (62), Expect = 3.6
Identities = 12/44 (27%), Positives = 21/44 (47%)
Query: 810 MILGLFMLTAGNFLGGVWANESWGRYWGWDPKETWALISICVYA 853
+ +G+ + AG+ L G WGRY W L+++ + A
Sbjct: 63 LTVGMIEMPAGHALAGEMVRSQWGRYLTWALSTPMILLALGLLA 106
>pdb|1PRG|A Chain A, Ligand Binding Domain Of The Human Peroxisome Proliferator
Activated Receptor Gamma
pdb|1PRG|B Chain B, Ligand Binding Domain Of The Human Peroxisome Proliferator
Activated Receptor Gamma
pdb|4PRG|A Chain A, 0072 Partial Agonist Ppar Gamma Cocrystal
pdb|4PRG|B Chain B, 0072 Partial Agonist Ppar Gamma Cocrystal
pdb|4PRG|C Chain C, 0072 Partial Agonist Ppar Gamma Cocrystal
pdb|4PRG|D Chain D, 0072 Partial Agonist Ppar Gamma Cocrystal
Length = 270
Score = 28.1 bits (61), Expect = 4.7
Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 1/84 (1%)
Query: 345 SFLLALILISPFTSSFANEAPI-DMHGGKSAKIERQSVENSAQKENSKSAILERLKRLRE 403
+ +A+I++S N PI D+ +E Q N + + +L+++ LR+
Sbjct: 179 AIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQ 238
Query: 404 YSKDHLKAFQRLQVQDFDGRIKPL 427
+H++ Q ++ + D + PL
Sbjct: 239 IVTEHVQLLQVIKKTETDMSLHPL 262
>pdb|3PRG|A Chain A, Ligand Binding Domain Of Human Peroxisome Proliferator
Activated Receptor
Length = 278
Score = 28.1 bits (61), Expect = 4.7
Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 1/84 (1%)
Query: 345 SFLLALILISPFTSSFANEAPI-DMHGGKSAKIERQSVENSAQKENSKSAILERLKRLRE 403
+ +A+I++S N PI D+ +E Q N + + +L+++ LR+
Sbjct: 186 AIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQ 245
Query: 404 YSKDHLKAFQRLQVQDFDGRIKPL 427
+H++ Q ++ + D + PL
Sbjct: 246 IVTEHVQLLQVIKKTETDMSLHPL 269
>pdb|1K74|D Chain D, The 2.3 Angstrom Resolution Crystal Structure Of The
Heterodimer Of The Human Ppargamma And Rxralpha Ligand
Binding Domains Respectively Bound With Gw409544 And
9-Cis Retinoic Acid And Co-Activator Peptides
Length = 283
Score = 28.1 bits (61), Expect = 4.7
Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 1/84 (1%)
Query: 345 SFLLALILISPFTSSFANEAPI-DMHGGKSAKIERQSVENSAQKENSKSAILERLKRLRE 403
+ +A+I++S N PI D+ +E Q N + + +L+++ LR+
Sbjct: 191 AIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQ 250
Query: 404 YSKDHLKAFQRLQVQDFDGRIKPL 427
+H++ Q ++ + D + PL
Sbjct: 251 IVTEHVQLLQVIKKTETDMSLHPL 274
>pdb|2PRG|A Chain A, Ligand-Binding Domain Of The Human Peroxisome Proliferator
Activated Receptor Gamma
pdb|2PRG|B Chain B, Ligand-Binding Domain Of The Human Peroxisome Proliferator
Activated Receptor Gamma
Length = 271
Score = 28.1 bits (61), Expect = 4.7
Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 1/84 (1%)
Query: 345 SFLLALILISPFTSSFANEAPI-DMHGGKSAKIERQSVENSAQKENSKSAILERLKRLRE 403
+ +A+I++S N PI D+ +E Q N + + +L+++ LR+
Sbjct: 179 AIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQ 238
Query: 404 YSKDHLKAFQRLQVQDFDGRIKPL 427
+H++ Q ++ + D + PL
Sbjct: 239 IVTEHVQLLQVIKKTETDMSLHPL 262
>pdb|1FM6|D Chain D, The 2.1 Angstrom Resolution Crystal Structure Of The
Heterodimer Of The Human Rxralpha And Ppargamma Ligand
Binding Domains Respectively Bound With 9-Cis Retinoic
Acid And Rosiglitazone And Co-Activator Peptides.
pdb|1FM9|D Chain D, The 2.1 Angstrom Resolution Crystal Structure Of The
Heterodimer Of The Human Rxralpha And Ppargamma Ligand
Binding Domains Respectively Bound With 9-Cis Retinoic
Acid And Gi262570 And Co-Activator Peptides.
pdb|1FM6|X Chain X, The 2.1 Angstrom Resolution Crystal Structure Of The
Heterodimer Of The Human Rxralpha And Ppargamma Ligand
Binding Domains Respectively Bound With 9-Cis Retinoic
Acid And Rosiglitazone And Co-Activator Peptides
Length = 272
Score = 28.1 bits (61), Expect = 4.7
Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 1/84 (1%)
Query: 345 SFLLALILISPFTSSFANEAPI-DMHGGKSAKIERQSVENSAQKENSKSAILERLKRLRE 403
+ +A+I++S N PI D+ +E Q N + + +L+++ LR+
Sbjct: 180 AIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQ 239
Query: 404 YSKDHLKAFQRLQVQDFDGRIKPL 427
+H++ Q ++ + D + PL
Sbjct: 240 IVTEHVQLLQVIKKTETDMSLHPL 263
>pdb|1I7I|A Chain A, Crystal Structure Of The Ligand Binding Domain Of Human
Ppar-Gamma In Complex With The Agonist Az 242
pdb|1I7I|B Chain B, Crystal Structure Of The Ligand Binding Domain Of Human
Ppar-Gamma In Complex With The Agonist Az 242
Length = 292
Score = 28.1 bits (61), Expect = 4.7
Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 1/84 (1%)
Query: 345 SFLLALILISPFTSSFANEAPI-DMHGGKSAKIERQSVENSAQKENSKSAILERLKRLRE 403
+ +A+I++S N PI D+ +E Q N + + +L+++ LR+
Sbjct: 200 AIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQ 259
Query: 404 YSKDHLKAFQRLQVQDFDGRIKPL 427
+H++ Q ++ + D + PL
Sbjct: 260 IVTEHVQLLQVIKKTETDMSLHPL 283
>pdb|1QHL|A Chain A, Crystal Structure Of The N-Terminal Domain Of Mukb At 2.2a
Resolution
Length = 227
Score = 27.3 bits (59), Expect = 8.0
Identities = 15/45 (33%), Positives = 22/45 (48%)
Query: 284 FFQSSYDMDEKGTILSVNKDPGKIPTYLGYAMLILGALWLLLDKN 328
FF ++D+DE T LS GK T + ++ L LL +N
Sbjct: 18 FFARTFDLDELVTTLSGGNGAGKSTTMAAFVTALIPDLTLLHFRN 62
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
0.324 0.139 0.409
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,062,356
Number of Sequences: 13198
Number of extensions: 206929
Number of successful extensions: 610
Number of sequences better than 10.0: 10
Number of HSP's better than 10.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 608
Number of HSP's gapped (non-prelim): 10
length of query: 936
length of database: 2,899,336
effective HSP length: 97
effective length of query: 839
effective length of database: 1,619,130
effective search space: 1358450070
effective search space used: 1358450070
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 59 (27.3 bits)