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|15644976|ref|NP_207146.1|
single-stranded-DNA-specific exonuclease (recJ) [Helicobacter pylori
26695]
(516 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|1IR6|A Chain A, Crystal Structure Of Exonuclease Recj B... 187 2e-48
pdb|1LKV|X Chain X, Crystal Structure Of The Middle And C-T... 28 1.9
pdb|1QC7|A Chain A, T. Maritima Flig C-Terminal Domain >gi|... 28 1.9
pdb|1HKS| Heat Shock Transcription Factor (Nmr, Restraine... 27 7.2
pdb|1DJN|A Chain A, Structural And Biochemical Characteriza... 27 7.2
pdb|1DJQ|A Chain A, Structural And Biochemical Characteriza... 27 7.2
pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoen... 26 9.4
pdb|1K9E|A Chain A, Crystal Structure Of A Mutated Family-6... 26 9.4
pdb|1K9D|A Chain A, The 1.7 A Crystal Structure Of Alpha-D-... 26 9.4
>pdb|1IR6|A Chain A, Crystal Structure Of Exonuclease Recj Bound To Manganese
Length = 424
Score = 187 bits (475), Expect = 2e-48
Identities = 140/429 (32%), Positives = 222/429 (51%), Gaps = 33/429 (7%)
Query: 30 KDLKKAALKIIEAMRTNTEILVVGDYDADGVISSAIMAKFFESLNYKHVRIAIPNRFMDG 89
K L++AA + EA+R I V GDYDADG+ +AI+ + +L V IP+R +G
Sbjct: 17 KGLREAAALLEEALRQGKRIRVHGDYDADGLTGTAILVRGLAALG-ADVHPFIPHRLEEG 75
Query: 90 YGISKKFLEKH--HAPLIITVDNGINAFEAARFCKEKNYTLIITDHHCLHHDEVPDAYAV 147
YG+ + + +H + L +TVD GI R E +I+TDHH + P V
Sbjct: 76 YGVLMERVPEHLEASDLFLTVDCGITNHAELRELLENGVEVIVTDHHT--PGKTPPPGLV 133
Query: 148 INPK-QPDCDFIQKEVCGALVAFYLCYGIHQLLGKEKSHSSELLCLAGVATIADMMPLTF 206
++P PD ++++ GA VAF L + +H+ LG E LA V TIAD+ PL
Sbjct: 134 VHPALTPD---LKEKPTGAGVAFLLLWALHERLGLPPP--LEYADLAAVGTIADVAPLWG 188
Query: 207 FNRFLVSKALYFLQKESLGAMGFLRQREVFRKRSLKASDISFNIAPLINSAGRMQDAKMA 266
+NR LV + L + S + L + + KA +++F IAP IN+A R+ +A+ A
Sbjct: 189 WNRALVKEGLARIPASSWVGLRLLAEAVGYTG---KAVEVAFRIAPRINAASRLGEAEKA 245
Query: 267 LDFLSANNSQDGYSLYERLKACNLKRKMIQQQVFEEAFKHAMVGEKIIVAFKDNWHEGVL 326
L L +++ + +L L N +R+ +++ + + A K IV H GV+
Sbjct: 246 LRLLLTDDAAEAQALVGELHRLNARRQTLEEAMLRKLLPQADPEAKAIVLLDPEGHPGVM 305
Query: 327 GIVASKLVEATQKPSLVFTFKEGVYKGSARSSSNIDLIDALNGVSSLLLGYGGHRQACGL 386
GIVAS+++EAT +P VF +G KG+ RS + I ++AL LLL YGGH++A G
Sbjct: 306 GIVASRILEATLRP--VFLVAQG--KGTVRSLAPISAVEALRSAEDLLLRYGGHKEAAGF 361
Query: 387 SVEKNNIISLFETLENFDFKVLPFCKTEPPLTLKLKDID--------RELLEIIEMGEPY 438
++++ +LF F +V + P ++ +D ++ + + EPY
Sbjct: 362 AMDE----ALFPA---FKARVEAYAARFPDPVREVALLDLLPEPGLLPQVFRELALLEPY 414
Query: 439 GQENPEPLF 447
G+ NPEPLF
Sbjct: 415 GEGNPEPLF 423
>pdb|1LKV|X Chain X, Crystal Structure Of The Middle And C-Terminal Domains Of
The Flagellar Rotor Protein Flig
Length = 232
Score = 28.5 bits (62), Expect = 1.9
Identities = 13/44 (29%), Positives = 26/44 (58%)
Query: 1 MKQKLKAQIKERMASIAYNEKGFPSPFLFKDLKKAALKIIEAMR 44
+K+K+ + +R A++ +E + P KD+++A KII +R
Sbjct: 169 LKEKIFKNMSKRAAALLKDELEYMGPVRLKDVEEAQQKIINIIR 212
>pdb|1QC7|A Chain A, T. Maritima Flig C-Terminal Domain
pdb|1QC7|B Chain B, T. Maritima Flig C-Terminal Domain
Length = 101
Score = 28.5 bits (62), Expect = 1.9
Identities = 13/44 (29%), Positives = 26/44 (58%)
Query: 1 MKQKLKAQIKERMASIAYNEKGFPSPFLFKDLKKAALKIIEAMR 44
+K+K+ + +R A++ +E + P KD+++A KII +R
Sbjct: 38 LKEKIFKNMSKRAAALLKDELEYMGPVRLKDVEEAQQKIINIIR 81
>pdb|1HKS| Heat Shock Transcription Factor (Nmr, Restrained Minimized Average
Structure)
pdb|1HKT| Heat Shock Transcription Factor (Nmr, 28 Structures)
Length = 106
Score = 26.6 bits (57), Expect = 7.2
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 10/74 (13%)
Query: 38 KIIEAMRTNTEILVVGDYDADGVISSAIMAKFFESLNYKHVRIAIPNRFMDGYGISKKFL 97
++++ TN I D + + + A AK LNYKH +A R ++ YG K
Sbjct: 13 RLVDDADTNRLICWTKDGQSFVIQNQAQFAKELLPLNYKHNNMASFIRQLNMYGFHK--- 69
Query: 98 EKHHAPLIITVDNG 111
I ++DNG
Sbjct: 70 -------ITSIDNG 76
>pdb|1DJN|A Chain A, Structural And Biochemical Characterization Of Recombinant
Wild Type Trimethylamine Dehydrogenase From
Methylophilus Methylotrophus (Sp. W3a1)
pdb|1DJN|B Chain B, Structural And Biochemical Characterization Of Recombinant
Wild Type Trimethylamine Dehydrogenase From
Methylophilus Methylotrophus (Sp. W3a1)
pdb|2TMD|A Chain A, Trimethylamine Dehydrogenase (E.C.1.5.99.7)
pdb|2TMD|B Chain B, Trimethylamine Dehydrogenase (E.C.1.5.99.7)
Length = 729
Score = 26.6 bits (57), Expect = 7.2
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 94 KKFLEKHHAPLIITVDNGINAFEAARFCKEKNYTLIITD 132
+KF + + ++ V G + EAAR E YT+ +TD
Sbjct: 381 EKFRQTKNKDSVLIVGAGPSGSEAARVLMESGYTVHLTD 419
>pdb|1DJQ|A Chain A, Structural And Biochemical Characterization Of Recombinant
C30a Mutant Of Trimethylamine Dehydrogenase From
Methylophilus Methylotrophus (Sp. W3a1)
pdb|1DJQ|B Chain B, Structural And Biochemical Characterization Of Recombinant
C30a Mutant Of Trimethylamine Dehydrogenase From
Methylophilus Methylotrophus (Sp. W3a1)
Length = 729
Score = 26.6 bits (57), Expect = 7.2
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 94 KKFLEKHHAPLIITVDNGINAFEAARFCKEKNYTLIITD 132
+KF + + ++ V G + EAAR E YT+ +TD
Sbjct: 381 EKFRQTKNKDSVLIVGAGPSGSEAARVLMESGYTVHLTD 419
>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 = 26.2 bits (56), Expect = 9.4
Identities = 19/60 (31%), Positives = 29/60 (47%), Gaps = 14/60 (23%)
Query: 431 IIEMGEPYGQENPEPLFQAKNLEVIEEKIIKESHQVLRFKDKECVKEAIYFSAERFLKAG 490
+ E+ EPY LF+A+ V+E K + E H + +++E V A FL AG
Sbjct: 242 LAELSEPY-------LFRAEESGVVELKDLAEGHLIYLRQEEEVV-------ARYFLPAG 287
>pdb|1K9E|A Chain A, Crystal Structure Of A Mutated Family-67 Alpha-D-
Glucuronidase (E285n) From Bacillus Stearothermophilus
T-6, Complexed With 4-O-Methyl-Glucuronic Acid
pdb|1K9F|A Chain A, Crystal Structure Of A Mutated Family-67 Alpha-D-
Glucuronidase (E285n) From Bacillus Stearothermophilus
T-6, Complexed With Aldotetraouronic Acid
Length = 679
Score = 26.2 bits (56), Expect = 9.4
Identities = 19/60 (31%), Positives = 27/60 (44%), Gaps = 2/60 (3%)
Query: 86 FMDGYGISKKFLEKHHAPLIITVDNGINAFEAARFCKEKNYTLIITDHHCLHHDEVPDAY 145
F+D + + K +A L+ +V GINA K T +ITDH EV D +
Sbjct: 168 FVDDQFVKQNQRIKDYARLLASV--GINAISINNVNVHKTETKLITDHFLPDVAEVADIF 225
>pdb|1K9D|A Chain A, The 1.7 A Crystal Structure Of Alpha-D-Glucuronidase, A
Family-67 Glycoside Hydrolase From Bacillus
Stearothermophilus T-1
Length = 679
Score = 26.2 bits (56), Expect = 9.4
Identities = 19/60 (31%), Positives = 27/60 (44%), Gaps = 2/60 (3%)
Query: 86 FMDGYGISKKFLEKHHAPLIITVDNGINAFEAARFCKEKNYTLIITDHHCLHHDEVPDAY 145
F+D + + K +A L+ +V GINA K T +ITDH EV D +
Sbjct: 168 FVDDQFVKQNQRIKDYARLLASV--GINAISINNVNVHKTETKLITDHFLPDVAEVADIF 225
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
0.321 0.138 0.393
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,778,864
Number of Sequences: 13198
Number of extensions: 112971
Number of successful extensions: 361
Number of sequences better than 10.0: 9
Number of HSP's better than 10.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 349
Number of HSP's gapped (non-prelim): 9
length of query: 516
length of database: 2,899,336
effective HSP length: 92
effective length of query: 424
effective length of database: 1,685,120
effective search space: 714490880
effective search space used: 714490880
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (26.2 bits)