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|15646179|ref|NP_208363.1| regulatory protein DniR
[Helicobacter pylori 26695]
(372 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|3SQC|A Chain A, Squalene-Hopene Cyclase >gi|5107753|pdb... 31 0.20
pdb|2SQC|A Chain A, Squalene-Hopene Cyclase From Alicycloba... 31 0.20
pdb|1SQC| Squalene-Hopene-Cyclase From Alicyclobacillus A... 31 0.20
pdb|1B34|A Chain A, Crystal Structure Of The D1d2 Sub-Compl... 28 2.2
pdb|1PNF| Pngase F Complex With Di-N-Acetylchitobiose >gi... 28 2.2
pdb|1PGS| Peptide-N(4)-(N-Acetyl-Beta-D-Glucosaminyl) Asp... 28 2.2
pdb|2SAS| Sarcoplasmic Calcium-Binding Protein (Iso Type Ii) 27 2.9
pdb|1IK3|A Chain A, Lipoxygenase-3 (Soybean) Complex With 1... 27 2.9
pdb|1JGI|A Chain A, Crystal Structure Of The Active Site Mu... 27 4.9
pdb|1G5A|A Chain A, Amylosucrase From Neisseria Polysacchar... 27 4.9
pdb|1B8A|A Chain A, Aspartyl-Trna Synthetase >gi|4388837|pd... 26 6.4
pdb|1HMJ|A Chain A, Solution Structure Of Rna Polymerase Su... 26 6.4
pdb|1RDR| Poliovirus 3d Polymerase 26 8.3
>pdb|3SQC|A Chain A, Squalene-Hopene Cyclase
pdb|3SQC|B Chain B, Squalene-Hopene Cyclase
pdb|3SQC|C Chain C, Squalene-Hopene Cyclase
Length = 631
Score = 31.2 bits (69), Expect = 0.20
Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 143 DPIKSTQAAITYLKRLYKQTGEWY-LVAMAYNYGLRKVQNAIKAAG 187
D K + A+ YLKR K G W+ + Y YG V +A+KA G
Sbjct: 463 DAWKVIRRAVEYLKREQKPDGSWFGRWGVNYLYGTGAVVSALKAVG 508
>pdb|2SQC|A Chain A, Squalene-Hopene Cyclase From Alicyclobacillus
Acidocaldarius
pdb|2SQC|B Chain B, Squalene-Hopene Cyclase From Alicyclobacillus
Acidocaldarius
Length = 631
Score = 31.2 bits (69), Expect = 0.20
Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 143 DPIKSTQAAITYLKRLYKQTGEWY-LVAMAYNYGLRKVQNAIKAAG 187
D K + A+ YLKR K G W+ + Y YG V +A+KA G
Sbjct: 463 DAWKVIRRAVEYLKREQKPDGSWFGRWGVNYLYGTGAVVSALKAVG 508
>pdb|1SQC| Squalene-Hopene-Cyclase From Alicyclobacillus Acidocaldarius
Length = 631
Score = 31.2 bits (69), Expect = 0.20
Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 143 DPIKSTQAAITYLKRLYKQTGEWY-LVAMAYNYGLRKVQNAIKAAG 187
D K + A+ YLKR K G W+ + Y YG V +A+KA G
Sbjct: 463 DAWKVIRRAVEYLKREQKPDGSWFGRWGVNYLYGTGAVVSALKAVG 508
>pdb|1B34|A Chain A, Crystal Structure Of The D1d2 Sub-Complex From The Human
Snrnp Core Domain
Length = 119
Score = 27.7 bits (60), Expect = 2.2
Identities = 22/75 (29%), Positives = 31/75 (41%), Gaps = 6/75 (8%)
Query: 233 LNRGARV--SLVGVPFKRRASLVQVAKNLN----LSLETLKSYNHQFRYNILPSKDPTYT 286
L G +V ++ GV L V L + LETL + RY ILP P T
Sbjct: 19 LKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDT 78
Query: 287 IYIPYEKLALFKQRQ 301
+ + E K+R+
Sbjct: 79 LLVDVEPKVKSKKRE 93
>pdb|1PNF| Pngase F Complex With Di-N-Acetylchitobiose
pdb|1PNG| Peptide-N(4)-(N-Acetyl-Beta-D-Glucosaminyl) Asparagine Amidase F
(Pngase F) (E.C.3.5.1.52)
Length = 314
Score = 27.7 bits (60), Expect = 2.2
Identities = 32/126 (25%), Positives = 57/126 (44%), Gaps = 12/126 (9%)
Query: 151 AITYLKRLYKQTGEWYLVA---MAYNYGLRKVQNAIKAAGTSDIKILLDEDKKYLPKETR 207
A Y+K K TGEWY + Y G K+ ++ +D K LL + + L T
Sbjct: 63 ANVYVKN--KTTGEWYEIGRFITPYWVGTEKLPRGLE-IDVTDFKSLLSGNTE-LKIYTE 118
Query: 208 EYIRSILSLALKFNSLDNLKDKEYL----LNRGARVSLVGVPFKRRASLVQVAKNLNLSL 263
++ ++ F+ + D +Y + + + S+ GVP+ +A + + KN+ L
Sbjct: 119 TWLAKGREYSVDFDIVYGTPDYKYSAVVPVIQYNKSSIDGVPY-GKAHTLGLKKNIQLPT 177
Query: 264 ETLKSY 269
T K+Y
Sbjct: 178 NTEKAY 183
>pdb|1PGS| Peptide-N(4)-(N-Acetyl-Beta-D-Glucosaminyl) Asparagine Amidase
(N-Glycosidase F) (Png-Ase F) (E.C.3.5.1.52)
Length = 314
Score = 27.7 bits (60), Expect = 2.2
Identities = 32/126 (25%), Positives = 57/126 (44%), Gaps = 12/126 (9%)
Query: 151 AITYLKRLYKQTGEWYLVA---MAYNYGLRKVQNAIKAAGTSDIKILLDEDKKYLPKETR 207
A Y+K K TGEWY + Y G K+ ++ +D K LL + + L T
Sbjct: 63 ANVYVKN--KTTGEWYEIGRFITPYWVGTEKLPRGLE-IDVTDFKSLLSGNTE-LKIYTE 118
Query: 208 EYIRSILSLALKFNSLDNLKDKEYL----LNRGARVSLVGVPFKRRASLVQVAKNLNLSL 263
++ ++ F+ + D +Y + + + S+ GVP+ +A + + KN+ L
Sbjct: 119 TWLAKGREYSVDFDIVYGTPDYKYSAVVPVIQYNKSSIDGVPY-GKAHTLGLKKNIQLPT 177
Query: 264 ETLKSY 269
T K+Y
Sbjct: 178 NTEKAY 183
>pdb|2SAS| Sarcoplasmic Calcium-Binding Protein (Iso Type Ii)
Length = 185
Score = 27.3 bits (59), Expect = 2.9
Identities = 17/67 (25%), Positives = 27/67 (39%)
Query: 10 QKWLVFFVTLLLASLGHAKMAFESDIDTKALEAFGVNAGFLSQMPNALKKMNKEEEWKRL 69
QK + F + H ++D + VN G LS + + E+EW+ L
Sbjct: 6 QKQKIKFTFDFFLDMNHDGSIQDNDFEDMMTRYKEVNKGSLSDADYKSMQASLEDEWRDL 65
Query: 70 VKRFDVN 76
R D+N
Sbjct: 66 KGRADIN 72
>pdb|1IK3|A Chain A, Lipoxygenase-3 (Soybean) Complex With
13(S)-Hydroperoxy-9(Z) ,11(E)-Octadecadienoic Acid
pdb|1BYT| Lipoxygenase-3 (Soybean) Complex With 4-Nitrocatechol
pdb|1LNH| Lipoxygenase-3(Soybean) Non-Heme Fe(Ii) Metalloprotein
Length = 857
Score = 27.3 bits (59), Expect = 2.9
Identities = 18/59 (30%), Positives = 28/59 (46%), Gaps = 1/59 (1%)
Query: 36 DTKALEAFGVNAGFLSQMPNALKKMNKEEEWKRLVKRFDVNYQ-FIPIIKNMLIEASVP 93
DT+ALEAF L+Q+ N L + N +E+ + + Y +P K L +P
Sbjct: 794 DTRALEAFKRFGNKLAQIENKLSERNNDEKLRNRCGPVQMPYTLLLPSSKEGLTFRGIP 852
>pdb|1JGI|A Chain A, Crystal Structure Of The Active Site Mutant Glu328gln Of
Amylosucrase From Neisseria Polysaccharea In Complex
With The Natural Substrate Sucrose
Length = 628
Score = 26.6 bits (57), Expect = 4.9
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 9/67 (13%)
Query: 54 PNALKKMNKEEEWKRLVKRFDVNYQFIPIIKNML------IEASVPQEFLFLAMAESKFS 107
P + K E+W++ +R D ++ P + N L EA +P + LA A +S
Sbjct: 17 PEQRAGIEKSEDWRQFSRRMDTHF---PKLMNELDSVYGNNEALLPMLEMLLAQAWQSYS 73
Query: 108 SRAYSRK 114
R S K
Sbjct: 74 QRNSSLK 80
>pdb|1G5A|A Chain A, Amylosucrase From Neisseria Polysaccharea
pdb|1JG9|A Chain A, Crystal Structure Of Amylosucrase From Neisseria
Polysaccharea In Complex With D-Glucose
Length = 628
Score = 26.6 bits (57), Expect = 4.9
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 9/67 (13%)
Query: 54 PNALKKMNKEEEWKRLVKRFDVNYQFIPIIKNML------IEASVPQEFLFLAMAESKFS 107
P + K E+W++ +R D ++ P + N L EA +P + LA A +S
Sbjct: 17 PEQRAGIEKSEDWRQFSRRMDTHF---PKLMNELDSVYGNNEALLPMLEMLLAQAWQSYS 73
Query: 108 SRAYSRK 114
R S K
Sbjct: 74 QRNSSLK 80
>pdb|1B8A|A Chain A, Aspartyl-Trna Synthetase
pdb|1B8A|B Chain B, Aspartyl-Trna Synthetase
Length = 438
Score = 26.2 bits (56), Expect = 6.4
Identities = 18/52 (34%), Positives = 24/52 (45%), Gaps = 3/52 (5%)
Query: 228 DKEYLLNRGARVSLVGVPFKRRASLVQVAKNLNLSLETLKSYNHQFRYNILP 279
D EY RG +S G R LV+ K L+ E+ + Y FRY + P
Sbjct: 354 DLEY---RGVEISSGGQREHRHDILVEQIKEKGLNPESFEFYLKAFRYGMPP 402
>pdb|1HMJ|A Chain A, Solution Structure Of Rna Polymerase Subunit H
Length = 78
Score = 26.2 bits (56), Expect = 6.4
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 319 HVVLPKETLSSIAKRYQVSISNI 341
H ++PKE + I KRY + I +
Sbjct: 12 HEIVPKEEVEEILKRYNIKIQQL 34
>pdb|1RDR| Poliovirus 3d Polymerase
Length = 461
Score = 25.8 bits (55), Expect = 8.3
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 6/73 (8%)
Query: 264 ETLKSYNHQFRYNILPSKDPTYTIYI-PYEKLALFK----QRQIKQNKNIQASSKSPFIT 318
+ + SY H+ ++L Y + + P +K A F+ + + +A K PF+
Sbjct: 329 DVIASYPHEVDASLLAQSGKDYGLTMTPADKSATFETVTWENVTFLKRFFRADEKYPFLI 388
Query: 319 HVVLP-KETLSSI 330
H V+P KE SI
Sbjct: 389 HPVMPMKEIHESI 401
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
0.320 0.134 0.376
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,843,306
Number of Sequences: 13198
Number of extensions: 67742
Number of successful extensions: 177
Number of sequences better than 10.0: 13
Number of HSP's better than 10.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 173
Number of HSP's gapped (non-prelim): 13
length of query: 372
length of database: 2,899,336
effective HSP length: 90
effective length of query: 282
effective length of database: 1,711,516
effective search space: 482647512
effective search space used: 482647512
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)