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|15645286|ref|NP_207456.1| ribonuclease III (rnc)
[Helicobacter pylori 26695]
(240 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|1JFZ|B Chain B, Crystal Structure Of Mn(Ii)-Complex Of ... 87 1e-18
pdb|1I4S|A Chain A, Crystal Structure Of Rnase Iii Endonucl... 87 1e-18
pdb|1QU6|A Chain A, Structure Of The Double-Stranded Rna-Bi... 39 5e-04
pdb|1DI2|A Chain A, Crystal Structure Of A Dsrna-Binding Do... 37 0.002
pdb|1EKZ|A Chain A, Nmr Structure Of The Complex Between Th... 28 0.72
pdb|1STU| Double Stranded Rna Binding Domain 28 0.72
pdb|1J7N|B Chain B, Anthrax Toxin Lethal Factor >gi|1697482... 28 1.2
pdb|1K75|A Chain A, The L-Histidinol Dehydrogenase (Hisd) S... 26 3.6
pdb|1KAE|A Chain A, L-Histidinol Dehydrogenase (Hisd) Struc... 26 3.6
pdb|1LA6|B Chain B, The Crystal Structure Of Trematomus New... 26 4.7
pdb|4HB1| A Designed Four Helix Bundle Protein 26 4.7
pdb|1IY9|A Chain A, Crystal Structure Of Spermidine Synthas... 25 8.0
>pdb|1JFZ|B Chain B, Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.10
Angstrom Resolution
pdb|1JFZ|C Chain C, Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.10
Angstrom Resolution
pdb|1JFZ|A Chain A, Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.10
Angstrom Resolution
pdb|1JFZ|D Chain D, Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.10
Angstrom Resolution
Length = 154
Score = 87.4 bits (215), Expect = 1e-18
Identities = 52/121 (42%), Positives = 71/121 (57%), Gaps = 6/121 (4%)
Query: 22 LEKALGYSFKDKRLLEQALTHKSCKLALNNERLEFLGDAVLGLVIGELLYHKFYQYDEGK 81
LEK LGY+FKDK LLE+ALTH S + E LEFLGDA++ I +LL EG
Sbjct: 8 LEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGF 67
Query: 82 LSKLRASIVSAHGFTKLAKAIALQDYLRVSSSEEISNGREKPSILSSAFEALMAGVYLEA 141
LS L+A ++S F LA+ + L ++R I G+ +I+ FEAL A VY+++
Sbjct: 68 LSPLKAYLISEEFFNLLAQKLELHKFIR------IKRGKINETIIGDVFEALWAAVYIDS 121
Query: 142 G 142
G
Sbjct: 122 G 122
>pdb|1I4S|A Chain A, Crystal Structure Of Rnase Iii Endonuclease Domain From
Aquifex Aeolicus At 2.15 Angstrom Resolution
pdb|1I4S|B Chain B, Crystal Structure Of Rnase Iii Endonuclease Domain From
Aquifex Aeolicus At 2.15 Angstrom Resolution
Length = 147
Score = 87.4 bits (215), Expect = 1e-18
Identities = 52/121 (42%), Positives = 71/121 (57%), Gaps = 6/121 (4%)
Query: 22 LEKALGYSFKDKRLLEQALTHKSCKLALNNERLEFLGDAVLGLVIGELLYHKFYQYDEGK 81
LEK LGY+FKDK LLE+ALTH S + E LEFLGDA++ I +LL EG
Sbjct: 7 LEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGF 66
Query: 82 LSKLRASIVSAHGFTKLAKAIALQDYLRVSSSEEISNGREKPSILSSAFEALMAGVYLEA 141
LS L+A ++S F LA+ + L ++R I G+ +I+ FEAL A VY+++
Sbjct: 67 LSPLKAYLISEEFFNLLAQKLELHKFIR------IKRGKINETIIGDVFEALWAAVYIDS 120
Query: 142 G 142
G
Sbjct: 121 G 121
>pdb|1QU6|A Chain A, Structure Of The Double-Stranded Rna-Binding Domain Of The
Protein Kinase Pkr Reveals The Molecular Basis Of Its
Dsrna Mediated Activation
Length = 179
Score = 38.9 bits (89), Expect = 5e-04
Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 184 VIPTYQLLKEKGPDHHKEFEMALYIQDKMYATAKGKSKKEAEQQCAYQALQKLKEAK 240
V+ YQ L GP H + F + I + + +G+SKKEA+ A A++ L + K
Sbjct: 28 VVLKYQELPNSGPPHDRRFTFQVIIDGREFPEGEGRSKKEAKNAAAKLAVEILNKEK 84
>pdb|1DI2|A Chain A, Crystal Structure Of A Dsrna-Binding Domain Complexed With
Dsrna: Molecular Basis Of Double-Stranded Rna-Protein
Interactions
pdb|1DI2|B Chain B, Crystal Structure Of A Dsrna-Binding Domain Complexed With
Dsrna: Molecular Basis Of Double-Stranded Rna-Protein
Interactions
Length = 69
Score = 37.4 bits (85), Expect = 0.002
Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 173 ALQELTQAQFCVIPTYQLLKEKGPDHHKEFEMALYIQDKMYATAKGKSKKEAEQQCAYQA 232
+LQEL + +P Y + +E GP H +EF + + + T G SK+ A++ A +
Sbjct: 5 SLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRV-ETFVETGSGTSKQVAKRVAAEKL 63
Query: 233 LQKLK 237
L K K
Sbjct: 64 LTKFK 68
>pdb|1EKZ|A Chain A, Nmr Structure Of The Complex Between The Third Dsrbd From
Drosophila Staufen And A Rna Hairpin
Length = 76
Score = 28.5 bits (62), Expect = 0.72
Identities = 15/51 (29%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 188 YQLLKEKGPDHHKEFEMALYIQDKMYATAKGKSKKEAEQQCAYQALQKLKE 238
+++L+E+GP H K F A I + +G KK ++++ A + L +L++
Sbjct: 26 FKVLREEGPAHMKNFITAC-IVGSIVTEGEGNGKKVSKKRAAEKMLVELQK 75
>pdb|1STU| Double Stranded Rna Binding Domain
Length = 68
Score = 28.5 bits (62), Expect = 0.72
Identities = 15/51 (29%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 188 YQLLKEKGPDHHKEFEMALYIQDKMYATAKGKSKKEAEQQCAYQALQKLKE 238
+++L+E+GP H K F A I + +G KK ++++ A + L +L++
Sbjct: 18 FKVLREEGPAHMKNFITAC-IVGSIVTEGEGNGKKVSKKRAAEKMLVELQK 67
>pdb|1J7N|B Chain B, Anthrax Toxin Lethal Factor
pdb|1J7N|A Chain A, Anthrax Toxin Lethal Factor
pdb|1JKY|A Chain A, Crystal Structure Of The Anthrax Lethal Factor (Lf): Wild-
Type Lf Complexed With The N-Terminal Sequence Of Mapkk2
Length = 776
Score = 27.7 bits (60), Expect = 1.2
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 10/76 (13%)
Query: 59 DAVLGLVIGELLYHKFYQYDEGKLSKLRAS----IVSAHGFTKLAKAIALQDYLR----- 109
DA+L IG LY+K Y Y+ ++ L A+ +V + TK+ + I ++ +
Sbjct: 420 DALLHQSIGSTLYNKIYLYENMNINNLTATLGADLVDSTDNTKINRGI-FNEFKKNFKYS 478
Query: 110 VSSSEEISNGREKPSI 125
+SS+ I + E+P++
Sbjct: 479 ISSNYMIVDINERPAL 494
>pdb|1K75|A Chain A, The L-Histidinol Dehydrogenase (Hisd) Structure Implicates
Domain Swapping And Gene Duplication.
pdb|1K75|B Chain B, The L-Histidinol Dehydrogenase (Hisd) Structure Implicates
Domain Swapping And Gene Duplication
Length = 434
Score = 26.2 bits (56), Expect = 3.6
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 89 IVSAHGFTKLAKAIALQDYLRVSSSEEISNGREKPSILSSAFEALMAGVYLEA 141
++ +G+T ++ L D+ + + +E+S +E S L+S E L A L A
Sbjct: 368 VLPTYGYTATCSSLGLADFQKRXTVQELS--KEGFSALASTIETLAAAERLTA 418
>pdb|1KAE|A Chain A, L-Histidinol Dehydrogenase (Hisd) Structure Complexed With
L-Histidinol (Substrate), Zinc And Nad (Cofactor)
pdb|1KAE|B Chain B, L-Histidinol Dehydrogenase (Hisd) Structure Complexed With
L-Histidinol (Substrate), Zinc And Nad (Cofactor)
pdb|1KAH|A Chain A, L-Histidinol Dehydrogenase (Hisd) Structure Complexed With
L-Histidine (Product), Zn And Nad (Cofactor)
pdb|1KAH|B Chain B, L-Histidinol Dehydrogenase (Hisd) Structure Complexed With
L-Histidine (Product), Zn And Nad (Cofactor)
pdb|1KAR|A Chain A, L-Histidinol Dehydrogenase (Hisd) Structure Complexed With
Histamine (Inhibitor), Zinc And Nad (Cofactor)
pdb|1KAR|B Chain B, L-Histidinol Dehydrogenase (Hisd) Structure Complexed With
Histamine (Inhibitor), Zinc And Nad (Cofactor)
Length = 434
Score = 26.2 bits (56), Expect = 3.6
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 89 IVSAHGFTKLAKAIALQDYLRVSSSEEISNGREKPSILSSAFEALMAGVYLEA 141
++ +G+T ++ L D+ + + +E+S +E S L+S E L A L A
Sbjct: 368 VLPTYGYTATCSSLGLADFQKRXTVQELS--KEGFSALASTIETLAAAERLTA 418
>pdb|1LA6|B Chain B, The Crystal Structure Of Trematomus Newnesi Hemoglobin In
A Partial Hemichrome State
pdb|1T1N|B Chain B, Crystal Structure Of Carbonmonoxy Hemoglobin
Length = 146
Score = 25.8 bits (55), Expect = 4.7
Identities = 16/54 (29%), Positives = 27/54 (49%), Gaps = 1/54 (1%)
Query: 41 THKSCKLALNNERLEFLGDAVLGLVIGELLYHKFYQYDEGKLSKLRASIVSAHG 94
T S KL ++ + + L D + +V+ + H F +G K A++VSA G
Sbjct: 90 TLHSEKLHVDPDNFKLLSDCIT-IVLAAKMGHAFTAETQGAFQKFLAAVVSALG 142
>pdb|4HB1| A Designed Four Helix Bundle Protein
Length = 108
Score = 25.8 bits (55), Expect = 4.7
Identities = 26/100 (26%), Positives = 44/100 (44%), Gaps = 8/100 (8%)
Query: 139 LEAGLAKVQKIMQNLLNRAYKRLDLEHLFMDYKTALQELTQAQFCVIPTYQLLKEKGPDH 198
L+ L + Q+++Q A K E L + A Q L QAQ L +KG
Sbjct: 6 LKQALQQAQQLLQQAQELAKKGGGEELLKQALQQAQQLLQQAQE--------LAKKGGGG 57
Query: 199 HKEFEMALYIQDKMYATAKGKSKKEAEQQCAYQALQKLKE 238
+ + AL ++ A+ +KK ++ QALQ+ ++
Sbjct: 58 EELLKQALQQAQQLLQQAQELAKKGGGEELLKQALQQAQQ 97
>pdb|1IY9|A Chain A, Crystal Structure Of Spermidine Synthase
pdb|1IY9|B Chain B, Crystal Structure Of Spermidine Synthase
pdb|1IY9|C Chain C, Crystal Structure Of Spermidine Synthase
pdb|1IY9|D Chain D, Crystal Structure Of Spermidine Synthase
Length = 275
Score = 25.0 bits (53), Expect = 8.0
Identities = 20/75 (26%), Positives = 31/75 (40%), Gaps = 3/75 (4%)
Query: 73 KFYQYDEGKLSKLRASIVSAHGFTKLAKAIALQDYLRVSSSEEISNGREKPSILSSAFEA 132
KF GKL R + GF +AK+ D + V S+E + ++ + F A
Sbjct: 117 KFLPSIAGKLDDPRVDVQVDDGFMHIAKSENQYDVIMVDSTEPVG---PAVNLFTKGFYA 173
Query: 133 LMAGVYLEAGLAKVQ 147
+A E G+ Q
Sbjct: 174 GIAKALKEDGIFVAQ 188
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
0.316 0.131 0.357
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,234,288
Number of Sequences: 13198
Number of extensions: 43563
Number of successful extensions: 135
Number of sequences better than 10.0: 12
Number of HSP's better than 10.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 128
Number of HSP's gapped (non-prelim): 12
length of query: 240
length of database: 2,899,336
effective HSP length: 86
effective length of query: 154
effective length of database: 1,764,308
effective search space: 271703432
effective search space used: 271703432
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)