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|15645845|ref|NP_208023.1| DNA polymerase III delta
prime subunit (holB) [Helicobacter pylori 26695]
(218 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|1JR3|E Chain E, Crystal Structure Of The Processivity C... 39 5e-04
pdb|1JR3|A Chain A, Crystal Structure Of The Processivity C... 37 0.002
pdb|1MFH|A Chain A, The Structure Of Bovine B-Lactoglobulin... 28 0.82
pdb|1CJ5|A Chain A, Bovine Beta-Lactoglobulin A >gi|7245834... 28 0.82
pdb|1BEB|A Chain A, Bovine Beta-Lactoglobulin, Lattice X >g... 28 1.1
pdb|1QLN|A Chain A, Structure Of A Transcribing T7 Rna Poly... 27 1.4
pdb|1ARO|P Chain P, T7 Rna Polymerase Complexed With T7 Lys... 27 1.4
pdb|1GX8|A Chain A, Bovine Beta-Lactoglobulin Complexed Wit... 27 1.8
pdb|1QEX|A Chain A, Bacteriophage T4 Gene Product 9 (Gp9), ... 26 3.1
pdb|1KLP|A Chain A, The Solution Structure Of Acyl Carrier ... 26 3.1
pdb|1QDS|A Chain A, Superstable E65q Mutant Of Leishmania M... 26 4.1
pdb|1IQP|A Chain A, Crystal Structure Of The Clamp Loader S... 26 4.1
pdb|1LXM|A Chain A, Crystal Structure Of Streptococcus Agal... 25 6.9
pdb|1AMK| Leishmania Mexicana Triose Phosphate Isomerase 25 9.1
>pdb|1JR3|E Chain E, Crystal Structure Of The Processivity Clamp Loader Gamma
Complex Of E. Coli Dna Polymerase Iii
pdb|1A5T| Crystal Structure Of The Delta Prime Subunit Of The Clamp-Loader
Complex Of Escherichia Coli Dna Polymerase Iii
Length = 334
Score = 38.9 bits (89), Expect = 5e-04
Identities = 29/94 (30%), Positives = 43/94 (44%), Gaps = 12/94 (12%)
Query: 27 HIKFYTEIIEKDKKVIKTFNKDFKIEHAKEVISKAHLKHSELNAFLIA----APSYGIEA 82
H +YT EK K + ++ +EV K + +H+ L + A A
Sbjct: 73 HPDYYTLAPEKGKNTLG-------VDAVREVTEKLN-EHARLGGAKVVWVTDAALLTDAA 124
Query: 83 QNALLKILEEPPNNVCFIMFAKSQNHVLATIKSR 116
NALLK LEEPP F + + +LAT++SR
Sbjct: 125 ANALLKTLEEPPAETWFFLATREPERLLATLRSR 158
>pdb|1JR3|A Chain A, Crystal Structure Of The Processivity Clamp Loader Gamma
Complex Of E. Coli Dna Polymerase Iii
pdb|1JR3|C Chain C, Crystal Structure Of The Processivity Clamp Loader Gamma
Complex Of E. Coli Dna Polymerase Iii
pdb|1JR3|B Chain B, Crystal Structure Of The Processivity Clamp Loader Gamma
Complex Of E. Coli Dna Polymerase Iii
Length = 373
Score = 36.6 bits (83), Expect = 0.002
Identities = 29/105 (27%), Positives = 48/105 (45%), Gaps = 12/105 (11%)
Query: 84 NALLKILEEPPNNVCFIMFAKSQNHVLATIKSRLIKEDKRQKIPLKPLDLDLSKLDLKDI 143
NALLK LEEPP +V F++ + TI SR + + LK LD++ + L+ I
Sbjct: 137 NALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCL------QFHLKALDVEQIRHQLEHI 190
Query: 144 YAFLKNLDKENFDSRENQRERIESLLESVNRHKIPLNEQELQAFD 188
L++E+ + + E R + L +Q + + D
Sbjct: 191 ------LNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGD 229
>pdb|1MFH|A Chain A, The Structure Of Bovine B-Lactoglobulin A In Crystals
Grown At Very Low Ionic Strength.
pdb|1MFH|B Chain B, The Structure Of Bovine B-Lactoglobulin A In Crystals
Grown At Very Low Ionic Strength.
pdb|1MFH|C Chain C, The Structure Of Bovine B-Lactoglobulin A In Crystals
Grown At Very Low Ionic Strength.
pdb|1MFH|D Chain D, The Structure Of Bovine B-Lactoglobulin A In Crystals
Grown At Very Low Ionic Strength.
pdb|1BSO|A Chain A, 12-Bromododecanoic Acid Binds Inside The Calyx Of Bovine
Beta-Lactoglobulin
pdb|1BSY| Structural Basis Of The Tanford Transition Of Bovine
Beta-Lactoglobulin From Crystal Structures At Three Ph
Values; Ph 7.1
pdb|2BLG| Structural Basis Of The Tanford Transition Of Bovine
Beta-Lactoglobulin From Crystal Structures At Three Ph
Values; Ph 8.2
pdb|3BLG| Structural Basis Of The Tanford Transition Of Bovine
Beta-Lactoglobulin From Crystal Structures At Three Ph
Values; Ph 6.2
pdb|1QG5|A Chain A, High Resolution Crystal Structure Of The Bovine Beta-
Lactoglobulin (Isoform A)
Length = 162
Score = 28.1 bits (61), Expect = 0.82
Identities = 31/128 (24%), Positives = 58/128 (45%), Gaps = 11/128 (8%)
Query: 80 IEAQNALLKI----LEEPPNNVCFIMFAKSQNHVLATIKSRLIKEDKRQKIPLKPLDLDL 135
++AQ+A L++ L+ P I+ K +N A + ++I E + KIP +
Sbjct: 32 LDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECA--QKKIIAE--KTKIPAV---FKI 84
Query: 136 SKLDLKDIYAFLKNLDKENFDSRENQRERIESLLESVNRHKIPLNEQELQAFDLAIKANS 195
L+ + + K EN E +SL+ ++++ L+ FD A+KA
Sbjct: 85 DALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALP 144
Query: 196 SYYKLSYN 203
+ +LS+N
Sbjct: 145 MHIRLSFN 152
>pdb|1CJ5|A Chain A, Bovine Beta-Lactoglobulin A
pdb|1DV9|A Chain A, Structural Changes Accompanying Ph-Induced Dissociation Of
The B-Lactoglobulin Dimer
Length = 162
Score = 28.1 bits (61), Expect = 0.82
Identities = 31/128 (24%), Positives = 58/128 (45%), Gaps = 11/128 (8%)
Query: 80 IEAQNALLKI----LEEPPNNVCFIMFAKSQNHVLATIKSRLIKEDKRQKIPLKPLDLDL 135
++AQ+A L++ L+ P I+ K +N A + ++I E + KIP +
Sbjct: 32 LDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECA--QKKIIAE--KTKIPAV---FKI 84
Query: 136 SKLDLKDIYAFLKNLDKENFDSRENQRERIESLLESVNRHKIPLNEQELQAFDLAIKANS 195
L+ + + K EN E +SL+ ++++ L+ FD A+KA
Sbjct: 85 DALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALP 144
Query: 196 SYYKLSYN 203
+ +LS+N
Sbjct: 145 MHIRLSFN 152
>pdb|1BEB|A Chain A, Bovine Beta-Lactoglobulin, Lattice X
pdb|1BEB|B Chain B, Bovine Beta-Lactoglobulin, Lattice X
Length = 162
Score = 27.7 bits (60), Expect = 1.1
Identities = 31/128 (24%), Positives = 58/128 (45%), Gaps = 11/128 (8%)
Query: 80 IEAQNALLKI----LEEPPNNVCFIMFAKSQNHVLATIKSRLIKEDKRQKIPLKPLDLDL 135
++AQ+A L++ L+ P I+ K +N A + ++I E + KIP +
Sbjct: 32 LDAQSAPLRVYVEELKPTPEGDLEILLQKWENGECA--QKKIIAE--KTKIPAV---FKI 84
Query: 136 SKLDLKDIYAFLKNLDKENFDSRENQRERIESLLESVNRHKIPLNEQELQAFDLAIKANS 195
L+ + + K EN E +SL+ ++++ L+ FD A+KA
Sbjct: 85 DALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALP 144
Query: 196 SYYKLSYN 203
+ +LS+N
Sbjct: 145 MHIRLSFN 152
>pdb|1QLN|A Chain A, Structure Of A Transcribing T7 Rna Polymerase Initiation
Complex
pdb|1CEZ|A Chain A, Crystal Structure Of A T7 Rna Polymerase-T7 Promoter
Complex
pdb|4RNP|A Chain A, Bacteriophage T7 Rna Polymerase, High Salt Crystal Form,
Low Temperature Data, Alpha-Carbons Only
pdb|4RNP|B Chain B, Bacteriophage T7 Rna Polymerase, High Salt Crystal Form,
Low Temperature Data, Alpha-Carbons Only
pdb|4RNP|C Chain C, Bacteriophage T7 Rna Polymerase, High Salt Crystal Form,
Low Temperature Data, Alpha-Carbons Only
Length = 883
Score = 27.3 bits (59), Expect = 1.4
Identities = 17/56 (30%), Positives = 33/56 (58%), Gaps = 7/56 (12%)
Query: 122 KRQKIPLKPLDLDLSKLDL---KDIYAFLKNLDKENFDSRENQRERIESLLESVNR 174
+R+++P+KP D+D++ L K A + DK +R+++R +E +LE N+
Sbjct: 356 EREELPMKPEDIDMNPEALTAWKRAAAAVYRKDK----ARKSRRISLEFMLEQANK 407
>pdb|1ARO|P Chain P, T7 Rna Polymerase Complexed With T7 Lysozyme
Length = 883
Score = 27.3 bits (59), Expect = 1.4
Identities = 17/56 (30%), Positives = 33/56 (58%), Gaps = 7/56 (12%)
Query: 122 KRQKIPLKPLDLDLSKLDL---KDIYAFLKNLDKENFDSRENQRERIESLLESVNR 174
+R+++P+KP D+D++ L K A + DK +R+++R +E +LE N+
Sbjct: 356 EREELPMKPEDIDMNPEALTAWKRAAAAVYRKDK----ARKSRRISLEFMLEQANK 407
>pdb|1GX8|A Chain A, Bovine Beta-Lactoglobulin Complexed With Retinol, Trigonal
Lattice Z
pdb|1GX9|A Chain A, Bovine Beta-Lactoglobulin Complexed With Retinoic Acid,
Trigonal Lattice Z
pdb|1GXA|A Chain A, Bovine Beta-Lactoglobulin Complexed With Retinol And
Palmitic Acid, Trigonal Lattice Z
pdb|1BSQ|A Chain A, Structural And Functional Consequences Of Point Mutations
Of Variants A And B Of Bovine Beta-Lactoglobulin
pdb|1B0O| Bovine Beta-Lactoglobulin Complexed With Palmitate, Lattice Z
pdb|1B8E|A Chain A, High Resolution Crystal Structure Of The Bovine Beta-
Lactoglobulin (Isoforms A And B) In Orthorombic Space
Group
Length = 162
Score = 26.9 bits (58), Expect = 1.8
Identities = 31/128 (24%), Positives = 57/128 (44%), Gaps = 11/128 (8%)
Query: 80 IEAQNALLKI----LEEPPNNVCFIMFAKSQNHVLATIKSRLIKEDKRQKIPLKPLDLDL 135
++AQ+A L++ L+ P I+ K +N A + ++I E + KIP +
Sbjct: 32 LDAQSAPLRVYVEELKPTPEGDLEILLQKWENGECA--QKKIIAE--KTKIPAV---FKI 84
Query: 136 SKLDLKDIYAFLKNLDKENFDSRENQRERIESLLESVNRHKIPLNEQELQAFDLAIKANS 195
L+ + + K EN E +SL ++++ L+ FD A+KA
Sbjct: 85 DALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALEKFDKALKALP 144
Query: 196 SYYKLSYN 203
+ +LS+N
Sbjct: 145 MHIRLSFN 152
>pdb|1QEX|A Chain A, Bacteriophage T4 Gene Product 9 (Gp9), The Trigger Of Tail
Contraction And The Long Tail Fibers Connector
pdb|1QEX|B Chain B, Bacteriophage T4 Gene Product 9 (Gp9), The Trigger Of Tail
Contraction And The Long Tail Fibers Connector
Length = 288
Score = 26.2 bits (56), Expect = 3.1
Identities = 15/57 (26%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 63 LKHSELNAFLIAAPSYGIEAQNALLKILEEPPNN-VCFIMFAKSQNHVLATIKSRLI 118
+K +E+N + S I ++ A++++ E + + I F+ +N+V ATI S +
Sbjct: 214 IKTAEINILVDTVNSEVISSEYAVMRVGNETEEDEIANIAFSIKENYVTATISSSTV 270
>pdb|1KLP|A Chain A, The Solution Structure Of Acyl Carrier Protein From
Mycobacterium Tuberculosis
Length = 115
Score = 26.2 bits (56), Expect = 3.1
Identities = 20/60 (33%), Positives = 36/60 (59%), Gaps = 6/60 (10%)
Query: 110 LATIKSRLIKEDKRQ-KIPLKPLDLDLSKL-DLKDIYAFLKNLDKENFDSRENQRERIES 167
L+ ++ + EDK KIP D DL+ L + D+ A+++ L++EN ++ + R +IES
Sbjct: 42 LSMVEIAVQTEDKYGVKIP----DEDLAGLRTVGDVVAYIQKLEEENPEAAQALRAKIES 97
>pdb|1QDS|A Chain A, Superstable E65q Mutant Of Leishmania Mexicana
Triosephosphate Isomerase (Tim)
pdb|1IF2|A Chain A, X-Ray Structure Of Leishmania Mexicana Triosephosphate
Isomerase Complexed With Ipp
Length = 251
Score = 25.8 bits (55), Expect = 4.1
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 39 KKVIKTFNKDFKIEHAKEVISKAHLKHSELNAFLIAAPSYGIEAQNALLK 88
+K+++ FN + I H + + H L + P Y I AQNA+ K
Sbjct: 23 EKLVQVFN-EHTISHDVQCVVAPTFVHIPLVQAKLRNPKYVISAQNAIAK 71
>pdb|1IQP|A Chain A, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|B Chain B, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|D Chain D, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|E Chain E, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|F Chain F, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|C Chain C, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
Length = 327
Score = 25.8 bits (55), Expect = 4.1
Identities = 15/46 (32%), Positives = 25/46 (53%)
Query: 71 FLIAAPSYGIEAQNALLKILEEPPNNVCFIMFAKSQNHVLATIKSR 116
FL A + +AQ AL + +E +NV FI+ + ++ I+SR
Sbjct: 115 FLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSR 160
>pdb|1LXM|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
Lyase Complexed With Hexasaccharide Unit Of Hyaluronan
pdb|1I8Q|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
Lyase Complexed With Enzyme Product, Unsaturated
Disaccharide Hyaluronan
pdb|1F1S|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
Lyase At 2.1 Angstrom Resolution
Length = 814
Score = 25.0 bits (53), Expect = 6.9
Identities = 23/94 (24%), Positives = 42/94 (44%), Gaps = 9/94 (9%)
Query: 91 EEPPNNVCFIMFAKSQNHVLATIKS----RLIKEDKRQKIPLKPLDLDLSKLDLK-DIYA 145
+EP N+ +I F S + ++ + + K I P K D K D Y
Sbjct: 663 KEPGRNIGYIFFKNSTIDIERKEQTGTWNSINRTSKNTSIVSNPFITISQKHDNKGDSYG 722
Query: 146 FLK--NLDKENFDSRENQRERIESLLESVNRHKI 177
++ N+D+ +FD N +E LLE+ ++ ++
Sbjct: 723 YMMVPNIDRTSFDKLANSKE--VELLENSSKQQV 754
>pdb|1AMK| Leishmania Mexicana Triose Phosphate Isomerase
Length = 251
Score = 24.6 bits (52), Expect = 9.1
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 39 KKVIKTFNKDFKIEHAKEVISKAHLKHSELNAFLIAAPSYGIEAQNALLK 88
+K+++ FN + I H + + H L + P Y I A+NA+ K
Sbjct: 23 EKLVQVFN-EHTISHDVQCVVAPTFVHIPLVQAKLRNPKYVISAENAIAK 71
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 0.134 0.358
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,093,784
Number of Sequences: 13198
Number of extensions: 41234
Number of successful extensions: 134
Number of sequences better than 10.0: 14
Number of HSP's better than 10.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 131
Number of HSP's gapped (non-prelim): 14
length of query: 218
length of database: 2,899,336
effective HSP length: 85
effective length of query: 133
effective length of database: 1,777,506
effective search space: 236408298
effective search space used: 236408298
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: 52 (24.6 bits)