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|15645558|ref|NP_207734.1| D-alanine glycine permease
(dagA) [Helicobacter pylori 26695]
(450 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|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoen... 30 0.43
pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-R... 30 0.43
pdb|1HQM|D Chain D, Crystal Structure Of Thermus Aquaticus ... 30 0.43
pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase... 28 2.1
pdb|1BG1|A Chain A, Three-Dimensional Structure Of The Stat... 27 3.6
pdb|1LB1|A Chain A, Crystal Structure Of The Dbl And Plecks... 27 3.6
pdb|1DBO|A Chain A, Crystal Structure Of Chondroitinase B >... 27 6.1
pdb|1ITH|A Chain A, Hemoglobin (Cyanomet) >gi|443052|pdb|1I... 26 8.0
pdb|1EP3|A Chain A, Crystal Structure Of Lactococcus Lactis... 26 8.0
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|M Chain M, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|D Chain D, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 1524
Score = 30.4 bits (67), Expect = 0.43
Identities = 19/48 (39%), Positives = 25/48 (51%), Gaps = 2/48 (4%)
Query: 69 LSLGATVGIGSIVGVATAISIAGPGAVFWM--WVTGLVGMATKYSEGI 114
LS+ V IG VGV A SI PG M + TG V + T ++G+
Sbjct: 1209 LSMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGL 1256
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 30.4 bits (67), Expect = 0.43
Identities = 19/48 (39%), Positives = 25/48 (51%), Gaps = 2/48 (4%)
Query: 69 LSLGATVGIGSIVGVATAISIAGPGAVFWM--WVTGLVGMATKYSEGI 114
LS+ V IG VGV A SI PG M + TG V + T ++G+
Sbjct: 949 LSMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGL 996
>pdb|1HQM|D Chain D, Crystal Structure Of Thermus Aquaticus Core Rna
Polymerase- Includes Complete Structure With Side-Chains
(Except For Disordered Regions)-Further Refined From
Original Deposition-Contains Additional Sequence
Information
Length = 1265
Score = 30.4 bits (67), Expect = 0.43
Identities = 19/48 (39%), Positives = 25/48 (51%), Gaps = 2/48 (4%)
Query: 69 LSLGATVGIGSIVGVATAISIAGPGAVFWM--WVTGLVGMATKYSEGI 114
LS+ V IG VGV A SI PG M + TG V + T ++G+
Sbjct: 950 LSMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGL 997
>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|N Chain N, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
Length = 1524
Score = 28.1 bits (61), Expect = 2.1
Identities = 18/48 (37%), Positives = 24/48 (49%), Gaps = 2/48 (4%)
Query: 69 LSLGATVGIGSIVGVATAISIAGPGAVFWM--WVTGLVGMATKYSEGI 114
LS+ V IG VG+ A SI PG M + TG V A ++G+
Sbjct: 1209 LSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGL 1256
>pdb|1BG1|A Chain A, Three-Dimensional Structure Of The Stat3b Homodimer Bound
To Dna
Length = 722
Score = 27.3 bits (59), Expect = 3.6
Identities = 8/23 (34%), Positives = 15/23 (64%)
Query: 88 SIAGPGAVFWMWVTGLVGMATKY 110
++AG G FW+W+ ++ + KY
Sbjct: 553 NMAGKGFSFWVWLDNIIDLVKKY 575
>pdb|1LB1|A Chain A, Crystal Structure Of The Dbl And Pleckstrin Homology
Domains Of Dbs In Complex With Rhoa
pdb|1LB1|C Chain C, Crystal Structure Of The Dbl And Pleckstrin Homology
Domains Of Dbs In Complex With Rhoa
pdb|1LB1|E Chain E, Crystal Structure Of The Dbl And Pleckstrin Homology
Domains Of Dbs In Complex With Rhoa
pdb|1LB1|G Chain G, Crystal Structure Of The Dbl And Pleckstrin Homology
Domains Of Dbs In Complex With Rhoa
Length = 353
Score = 27.3 bits (59), Expect = 3.6
Identities = 12/32 (37%), Positives = 16/32 (49%)
Query: 110 YSEGILAVKYREKGAFGYNGGPMYYIKNGLNM 141
+ + +L K RE+ GY P Y K LNM
Sbjct: 245 HEKAVLFCKKREENGEGYEKAPSYSYKQSLNM 276
>pdb|1DBO|A Chain A, Crystal Structure Of Chondroitinase B
pdb|1DBG|A Chain A, Crystal Structure Of Chondroitinase B
Length = 506
Score = 26.6 bits (57), Expect = 6.1
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 199 IKSIGKFTSYLAPVMVLLYLIAIIYIIVSHFDLALQAIK 237
+K + K YL P+MVLL + + +V+ + Q +K
Sbjct: 1 MKMLNKLAGYLLPIMVLLNVAPCLGQVVASNETLYQVVK 39
>pdb|1ITH|A Chain A, Hemoglobin (Cyanomet)
pdb|1ITH|B Chain B, Hemoglobin (Cyanomet)
Length = 141
Score = 26.2 bits (56), Expect = 8.0
Identities = 14/42 (33%), Positives = 21/42 (49%), Gaps = 4/42 (9%)
Query: 224 IIVSHFDLALQAIKLIFEEAFNPKPVV----GGASGALIATM 261
I HF L+ + +F+E F+ P G A+G L+A M
Sbjct: 99 ITPKHFGQLLKLVGGVFQEEFSADPTTVAAWGDAAGVLVAAM 140
>pdb|1EP3|A Chain A, Crystal Structure Of Lactococcus Lactis Dihydroorotate
Dehydrogenase B. Data Collected Under Cryogenic
Conditions.
pdb|1EP1|A Chain A, Crystal Structure Of Lactococcus Lactis Dihydroorotate
Dehydrogenase B
pdb|1EP2|A Chain A, Crystal Structure Of Lactococcus Lactis Dihydroorotate
Dehydrogenase B Complexed With Orotate
Length = 311
Score = 26.2 bits (56), Expect = 8.0
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 381 YAFGEKKVKYYRLIFLASVMVGA 403
+ FGE+ KYY L L S+MV A
Sbjct: 27 FGFGEEYAKYYDLNKLGSIMVKA 49
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 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,316,764
Number of Sequences: 13198
Number of extensions: 89541
Number of successful extensions: 313
Number of sequences better than 10.0: 9
Number of HSP's better than 10.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 305
Number of HSP's gapped (non-prelim): 10
length of query: 450
length of database: 2,899,336
effective HSP length: 91
effective length of query: 359
effective length of database: 1,698,318
effective search space: 609696162
effective search space used: 609696162
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (26.2 bits)