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|15645311|ref|NP_207482.1| hypothetical protein
[Helicobacter pylori 26695]
(166 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|1D5A|A Chain A, Crystal Structure Of An Archaebacterial... 33 0.022
pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial... 33 0.022
pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From... 32 0.049
pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9o... 30 0.11
pdb|1GCX|A Chain A, Crystal Structure Of Family B Dna Polym... 29 0.24
pdb|1CLQ|A Chain A, Crystal Structure Of A Replication Fork... 29 0.32
pdb|1IG9|A Chain A, Structure Of The Replicating Complex Of... 26 2.7
pdb|1DTN| Mandelate Racemase Mutant D270n Co-Crystallized... 25 4.6
pdb|1EXI|A Chain A, Crystal Structure Of Transcription Acti... 25 4.6
pdb|1MRA| Mandelate Racemase Mutant D270n Co-Crystallized... 25 4.6
pdb|1MDR| Mandelate Racemase (E.C.5.1.2.2) 25 4.6
pdb|2MNR| Mandelate Racemase (E.C.5.1.2.2) >gi|443131|pdb... 25 4.6
pdb|1M31|A Chain A, Three-Dimensional Solution Structure Of... 25 6.0
pdb|1EP1|B Chain B, Crystal Structure Of Lactococcus Lactis... 25 6.0
pdb|1EP3|B Chain B, Crystal Structure Of Lactococcus Lactis... 25 6.0
pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box... 24 7.8
>pdb|1D5A|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok. Deposition Of Second Native Structure At 2.4
Angstro
Length = 733
Score = 32.7 bits (73), Expect = 0.022
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 82 EDFTSEKELLEDFFKYFNEKQPR-LISFNGRGFDMPLL 118
E ++EKE+++ F K EK P LI++NG FD L
Sbjct: 182 ESVSTEKEMIKRFLKVIQEKDPDVLITYNGDNFDFAYL 219
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok
Length = 773
Score = 32.7 bits (73), Expect = 0.022
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 82 EDFTSEKELLEDFFKYFNEKQPR-LISFNGRGFDMPLL 118
E ++EKE+++ F K EK P LI++NG FD L
Sbjct: 182 ESVSTEKEMIKRFLKVIQEKDPDVLITYNGDNFDFAYL 219
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 31.6 bits (70), Expect = 0.049
Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 85 TSEKELLEDFFKYFNEKQPR-LISFNGRGFDMPLLTLKALK 124
++EKE+++ F K EK P LI++NG FD L ++ K
Sbjct: 185 STEKEMIKRFLKVVKEKDPDVLITYNGDNFDFAYLKKRSEK 225
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
Score = 30.4 bits (67), Expect = 0.11
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 85 TSEKELLEDFFKYFNEKQPR-LISFNGRGFDMPLLTLK----ALKYNLTLDAFYNQ-ENK 138
++EKE+++ F + EK P LI++NG FD L + +K+ L D + +
Sbjct: 185 STEKEMIKRFLRVVREKDPDVLITYNGDNFDFAYLKKRCEELGIKFTLGRDGSEPKIQRM 244
Query: 139 WENYRARYSEQFHLDL 154
+ + + H DL
Sbjct: 245 GDRFAVEVKGRIHFDL 260
Score = 25.4 bits (54), Expect = 3.5
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 83 DFTSEKELLEDFFKYFNEKQPRLISFNGRGF 113
D + K+ ++F KY N K P L+ GF
Sbjct: 552 DAETVKKKAKEFLKYINPKLPGLLELEYEGF 582
>pdb|1GCX|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 29.3 bits (64), Expect = 0.24
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 85 TSEKELLEDFFKYFNEKQPR-LISFNGRGFDMPLLTLKALKYNL 127
++E+E+++ F + EK P LI++NG FD L + K +
Sbjct: 185 STEREMIKRFLRVVKEKDPDVLITYNGDNFDFAYLKKRCEKLGI 228
>pdb|1CLQ|A Chain A, Crystal Structure Of A Replication Fork Dna Polymerase
Editing Complex At 2.7 A Resolution
pdb|1WAJ| Dna Polymerase From Bacteriophage Rb69
pdb|1WAF|A Chain A, Dna Polymerase From Bacteriophage Rb69
pdb|1WAF|B Chain B, Dna Polymerase From Bacteriophage Rb69
pdb|1IH7|A Chain A, High-Resolution Structure Of Apo Rb69 Dna Polymerase
Length = 903
Score = 28.9 bits (63), Expect = 0.32
Identities = 12/34 (35%), Positives = 23/34 (67%), Gaps = 1/34 (2%)
Query: 84 FTSEKELLEDFFKYFNEKQPRLIS-FNGRGFDMP 116
F +EKELL ++ ++ +K P +++ +N FD+P
Sbjct: 191 FDNEKELLMEYLNFWQQKTPVILTGWNVESFDIP 224
>pdb|1IG9|A Chain A, Structure Of The Replicating Complex Of A Pol Alpha Family
Dna Polymerase
Length = 903
Score = 25.8 bits (55), Expect = 2.7
Identities = 11/34 (32%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 84 FTSEKELLEDFFKYFNEKQPRLIS-FNGRGFDMP 116
F +EKELL ++ ++ +K P +++ +N F +P
Sbjct: 191 FDNEKELLMEYLNFWQQKTPVILTGWNVESFAIP 224
>pdb|1DTN| Mandelate Racemase Mutant D270n Co-Crystallized With
(S)-Atrolactate
Length = 359
Score = 25.0 bits (53), Expect = 4.6
Identities = 17/62 (27%), Positives = 25/62 (39%), Gaps = 7/62 (11%)
Query: 5 FDIETIPNISLCKEHFQLEENDALKICEWSFEKQKEKSGSEFLPLYLHEIISIAAVIGDD 64
+D ++ + L E A+ E F K K G L L + SI +GDD
Sbjct: 137 YDSHSLDGVKLATER-------AVTAAELGFRAVKTKIGYPALDQDLAVVRSIRQAVGDD 189
Query: 65 YG 66
+G
Sbjct: 190 FG 191
>pdb|1EXI|A Chain A, Crystal Structure Of Transcription Activator Bmrr, From B.
Subtilis, Bound To 21 Base Pair Bmr Operator And Tpsb
pdb|1EXJ|A Chain A, Crystal Structure Of Transcription Activator Bmrr, From B.
Subtilis, Bound To 21 Base Pair Bmr Operator And Tpp
Length = 278
Score = 25.0 bits (53), Expect = 4.6
Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 6/50 (12%)
Query: 118 LTLKALKYNLTLD----AFYNQENKWENYRARYSEQFHLDLMDSLSHYGS 163
+++KAL+Y +D A+ + + + Y S+ HLDL+ SL + G+
Sbjct: 17 VSIKALRYYDKIDLFKPAYVDPDTSYRYYTD--SQLIHLDLIKSLKYIGT 64
>pdb|1MRA| Mandelate Racemase Mutant D270n Co-Crystallized With
(S)-Atrolactate
Length = 359
Score = 25.0 bits (53), Expect = 4.6
Identities = 17/62 (27%), Positives = 25/62 (39%), Gaps = 7/62 (11%)
Query: 5 FDIETIPNISLCKEHFQLEENDALKICEWSFEKQKEKSGSEFLPLYLHEIISIAAVIGDD 64
+D ++ + L E A+ E F K K G L L + SI +GDD
Sbjct: 137 YDSHSLDGVKLATER-------AVTAAELGFRAVKTKIGYPALDQDLAVVRSIRQAVGDD 189
Query: 65 YG 66
+G
Sbjct: 190 FG 191
>pdb|1MDR| Mandelate Racemase (E.C.5.1.2.2)
Length = 359
Score = 25.0 bits (53), Expect = 4.6
Identities = 17/62 (27%), Positives = 25/62 (39%), Gaps = 7/62 (11%)
Query: 5 FDIETIPNISLCKEHFQLEENDALKICEWSFEKQKEKSGSEFLPLYLHEIISIAAVIGDD 64
+D ++ + L E A+ E F K K G L L + SI +GDD
Sbjct: 137 YDSHSLDGVKLATER-------AVTAAELGFRAVKTKIGYPALDQDLAVVRSIRQAVGDD 189
Query: 65 YG 66
+G
Sbjct: 190 FG 191
>pdb|2MNR| Mandelate Racemase (E.C.5.1.2.2)
pdb|1MNS| Mandelate Racemase (E.C.5.1.2.2)
Length = 357
Score = 25.0 bits (53), Expect = 4.6
Identities = 17/62 (27%), Positives = 25/62 (39%), Gaps = 7/62 (11%)
Query: 5 FDIETIPNISLCKEHFQLEENDALKICEWSFEKQKEKSGSEFLPLYLHEIISIAAVIGDD 64
+D ++ + L E A+ E F K K G L L + SI +GDD
Sbjct: 135 YDSHSLDGVKLATER-------AVTAAELGFRAVKTKIGYPALDQDLAVVRSIRQAVGDD 187
Query: 65 YG 66
+G
Sbjct: 188 FG 189
>pdb|1M31|A Chain A, Three-Dimensional Solution Structure Of Apo-Mts1
pdb|1M31|B Chain B, Three-Dimensional Solution Structure Of Apo-Mts1
Length = 101
Score = 24.6 bits (52), Expect = 6.0
Identities = 24/92 (26%), Positives = 34/92 (36%), Gaps = 14/92 (15%)
Query: 27 ALKICEWSFEKQKEKSG-------SEFLPLYLHEIISIAAVIGDDYGQFIKVGNFGQKHE 79
AL + +F K K G SE L E+ S D+ + N +
Sbjct: 8 ALDVMVSTFHKYSGKEGDKFKLNKSELKELLTRELPSFLGKRTDEAAFQKLMSNLDSNRD 67
Query: 80 NKEDFTSEKELLE-------DFFKYFNEKQPR 104
N+ DF L +FF+ F +KQPR
Sbjct: 68 NEVDFQEYCVFLSCIAMMCNEFFEGFPDKQPR 99
>pdb|1EP1|B Chain B, Crystal Structure Of Lactococcus Lactis Dihydroorotate
Dehydrogenase B
pdb|1EP2|B Chain B, Crystal Structure Of Lactococcus Lactis Dihydroorotate
Dehydrogenase B Complexed With Orotate
Length = 261
Score = 24.6 bits (52), Expect = 6.0
Identities = 9/17 (52%), Positives = 13/17 (75%)
Query: 16 CKEHFQLEENDALKICE 32
C EH + +E+ ALK+CE
Sbjct: 233 CVEHDKEDESHALKVCE 249
>pdb|1EP3|B Chain B, Crystal Structure Of Lactococcus Lactis Dihydroorotate
Dehydrogenase B. Data Collected Under Cryogenic
Conditions
Length = 262
Score = 24.6 bits (52), Expect = 6.0
Identities = 9/17 (52%), Positives = 13/17 (75%)
Query: 16 CKEHFQLEENDALKICE 32
C EH + +E+ ALK+CE
Sbjct: 234 CVEHDKEDESHALKVCE 250
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human Upstream
Binding Factor
Length = 99
Score = 24.3 bits (51), Expect = 7.8
Identities = 17/78 (21%), Positives = 36/78 (45%), Gaps = 9/78 (11%)
Query: 88 KELLEDFFKYFNEKQPRLISFNGRGFDMPLLTLKALKYN--------LTLDAFYNQENKW 139
K+ L +F++F EK+ + + ++ L + + KY + F ++ ++
Sbjct: 12 KKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEF 71
Query: 140 ENYRARYSEQFHLDLMDS 157
E AR+ E H DL+ +
Sbjct: 72 ERNLARFRED-HPDLIQN 88
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 0.139 0.416
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,058,029
Number of Sequences: 13198
Number of extensions: 44305
Number of successful extensions: 99
Number of sequences better than 10.0: 16
Number of HSP's better than 10.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 84
Number of HSP's gapped (non-prelim): 22
length of query: 166
length of database: 2,899,336
effective HSP length: 81
effective length of query: 85
effective length of database: 1,830,298
effective search space: 155575330
effective search space used: 155575330
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: 51 (24.3 bits)