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|15645970|ref|NP_208150.1| hypothetical protein
[Helicobacter pylori 26695]
(168 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|2HMX| Human Immunodeficiency Virus Type 1 Matrix Prot... 33 0.022
pdb|1L6N|A Chain A, Structure Of The N-Terminal 283-Residue... 33 0.022
pdb|2TMA|A Chain A, Tropomyosin >gi|230768|pdb|2TMA|B Chain... 28 0.41
pdb|1C1G|A Chain A, Crystal Structure Of Tropomyosin At 7 A... 28 0.71
pdb|1RES| Gamma Delta Resolvase (Dna Binding Domain) (Nmr... 27 1.6
pdb|1GDT|A Chain A, Crystal Structure Of A Site-Specific Re... 27 1.6
pdb|1I01|E Chain E, Crystal Structure Of Beta-Ketoacyl [acy... 26 2.1
pdb|1F1M|A Chain A, Crystal Structure Of Outer Surface Prot... 26 2.1
pdb|1M6N|A Chain A, Crystal Structure Of The Seca Transloca... 26 2.7
pdb|1QHH|B Chain B, Structure Of Dna Helicase With Adpnp 25 3.5
pdb|3PJR|A Chain A, Helicase Substrate Complex >gi|2781090|... 25 3.5
pdb|2PJR|F Chain F, Helicase Product Complex >gi|9257172|pd... 25 3.5
pdb|1K3E|B Chain B, Type Iii Secretion Chaperone Cest >gi|1... 25 4.6
pdb|1GTM|A Chain A, Structure Of Glutamate Dehydrogenase >g... 25 4.6
pdb|1MU2|B Chain B, Crystal Structure Of Hiv-2 Reverse Tran... 25 6.0
pdb|1MU2|A Chain A, Crystal Structure Of Hiv-2 Reverse Tran... 25 6.0
pdb|1GE9|A Chain A, Solution Structure Of The Ribosome Recy... 24 7.8
pdb|1K9X|A Chain A, Structure Of Pyrococcus Furiosus Carbox... 24 7.8
>pdb|2HMX| Human Immunodeficiency Virus Type 1 Matrix Protein
pdb|1HIW|A Chain A, Trimeric Hiv-1 Matrix Protein
pdb|1HIW|R Chain R, Trimeric Hiv-1 Matrix Protein
pdb|1HIW|C Chain C, Trimeric Hiv-1 Matrix Protein
pdb|1HIW|B Chain B, Trimeric Hiv-1 Matrix Protein
pdb|1HIW|Q Chain Q, Trimeric Hiv-1 Matrix Protein
pdb|1HIW|S Chain S, Trimeric Hiv-1 Matrix Protein
Length = 133
Score = 32.7 bits (73), Expect = 0.022
Identities = 28/84 (33%), Positives = 44/84 (52%), Gaps = 6/84 (7%)
Query: 55 SKRLKELEGRLEGLSLEKSAKEDSSLKTTLSHLYNQLQEIQKSMDKER-DYLEEKIITLE 113
S+ +++ G+L+ SL+ ++E SL T++ LY Q I KE D +EE+ +
Sbjct: 55 SEGCRQILGQLQP-SLQTGSEELRSLYNTIAVLYCVHQRIDVKDTKEALDKIEEE----Q 109
Query: 114 NKFKDMGHYAASDEINEKQVLKMY 137
NK K AA+D N QV + Y
Sbjct: 110 NKSKKKAQQAAADTGNNSQVSQNY 133
>pdb|1L6N|A Chain A, Structure Of The N-Terminal 283-Residue Fragment Of The
Hiv- 1 Gag Polyprotein
Length = 289
Score = 32.7 bits (73), Expect = 0.022
Identities = 28/84 (33%), Positives = 44/84 (52%), Gaps = 6/84 (7%)
Query: 55 SKRLKELEGRLEGLSLEKSAKEDSSLKTTLSHLYNQLQEIQKSMDKER-DYLEEKIITLE 113
S+ +++ G+L+ SL+ ++E SL T++ LY Q I KE D +EE+ +
Sbjct: 54 SEGCRQILGQLQP-SLQTGSEELRSLYNTIAVLYCVHQRIDVKDTKEALDKIEEE----Q 108
Query: 114 NKFKDMGHYAASDEINEKQVLKMY 137
NK K AA+D N QV + Y
Sbjct: 109 NKSKKKAQQAAADTGNNSQVSQNY 132
>pdb|2TMA|A Chain A, Tropomyosin
pdb|2TMA|B Chain B, Tropomyosin
Length = 284
Score = 28.5 bits (62), Expect = 0.41
Identities = 19/89 (21%), Positives = 45/89 (50%), Gaps = 5/89 (5%)
Query: 29 KEKEFYHKMRRLEKTLDESYQENYIYSKRLKELEGRLEGLSLEKSAKEDSSLKTTLSHLY 88
+ K+ ++ L+K L + E YS+ LK+ + + LE + K+ + + ++ L
Sbjct: 35 RSKQLEDELVSLQKKLKGTEDELDKYSEALKDAQEK-----LELAEKKATDAEADVASLN 89
Query: 89 NQLQEIQKSMDKERDYLEEKIITLENKFK 117
++Q +++ +D+ ++ L + LE K
Sbjct: 90 RRIQLVEEELDRAQERLATALQKLEEAEK 118
>pdb|1C1G|A Chain A, Crystal Structure Of Tropomyosin At 7 Angstroms Resolution
In The Spermine-Induced Crystal Form
pdb|1C1G|B Chain B, Crystal Structure Of Tropomyosin At 7 Angstroms Resolution
In The Spermine-Induced Crystal Form
pdb|1C1G|C Chain C, Crystal Structure Of Tropomyosin At 7 Angstroms Resolution
In The Spermine-Induced Crystal Form
pdb|1C1G|D Chain D, Crystal Structure Of Tropomyosin At 7 Angstroms Resolution
In The Spermine-Induced Crystal Form
Length = 284
Score = 27.7 bits (60), Expect = 0.71
Identities = 19/89 (21%), Positives = 44/89 (49%), Gaps = 5/89 (5%)
Query: 29 KEKEFYHKMRRLEKTLDESYQENYIYSKRLKELEGRLEGLSLEKSAKEDSSLKTTLSHLY 88
+ K+ ++ L+K L + E YS+ LK+ + + LE + K+ + + ++ L
Sbjct: 35 RSKQLEDELVSLQKKLKATEDELDKYSEALKDAQEK-----LELAEKKATDAEADVASLN 89
Query: 89 NQLQEIQKSMDKERDYLEEKIITLENKFK 117
++Q ++ +D+ ++ L + LE K
Sbjct: 90 RRIQLFEEELDRAQERLATALQKLEEAEK 118
>pdb|1RES| Gamma Delta Resolvase (Dna Binding Domain) (Nmr, Minimized Mean
Structure)
pdb|1RET| Gamma Delta Resolvase (Dna Binding Domain) (Nmr, 17 Structures)
Length = 43
Score = 26.6 bits (57), Expect = 1.6
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 127 EINEKQVLKMYQEGYSVDSISKEFKVSKGEVEFILN 162
+I+ VL M+Q+G ISK +++ V ++N
Sbjct: 5 KIDRDAVLNMWQQGLGASHISKTMNIARSTVYKVIN 40
>pdb|1GDT|A Chain A, Crystal Structure Of A Site-Specific Recombinase,
Gamma-Delta Resolvase Complexed With A 34 Bp Cleavage
Site
pdb|1GDT|B Chain B, Crystal Structure Of A Site-Specific Recombinase,
Gamma-Delta Resolvase Complexed With A 34 Bp Cleavage
Site
Length = 183
Score = 26.6 bits (57), Expect = 1.6
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 127 EINEKQVLKMYQEGYSVDSISKEFKVSKGEVEFILN 162
+I+ VL M+Q+G ISK +++ V ++N
Sbjct: 145 KIDRDAVLNMWQQGLGASHISKTMNIARSTVYKVIN 180
>pdb|1I01|E Chain E, Crystal Structure Of Beta-Ketoacyl [acyl Carrier Protein]
Reductase From E. Coli.
pdb|1I01|B Chain B, Crystal Structure Of Beta-Ketoacyl [acyl Carrier Protein]
Reductase From E. Coli.
pdb|1I01|A Chain A, Crystal Structure Of Beta-Ketoacyl [acyl Carrier Protein]
Reductase From E. Coli.
pdb|1I01|F Chain F, Crystal Structure Of Beta-Ketoacyl [acyl Carrier Protein]
Reductase From E. Coli.
pdb|1I01|D Chain D, Crystal Structure Of Beta-Ketoacyl [acyl Carrier Protein]
Reductase From E. Coli.
pdb|1I01|G Chain G, Crystal Structure Of Beta-Ketoacyl [acyl Carrier Protein]
Reductase From E. Coli.
pdb|1I01|H Chain H, Crystal Structure Of Beta-Ketoacyl [acyl Carrier Protein]
Reductase From E. Coli.
pdb|1I01|C Chain C, Crystal Structure Of Beta-Ketoacyl [acyl Carrier Protein]
Reductase From E. Coli
Length = 244
Score = 26.2 bits (56), Expect = 2.1
Identities = 14/49 (28%), Positives = 28/49 (56%), Gaps = 2/49 (4%)
Query: 120 GHYAASDEI--NEKQVLKMYQEGYSVDSISKEFKVSKGEVEFILNMAGL 166
G A SD + N K ++ + S++S+ ++ + GEV+ ++N AG+
Sbjct: 41 GAQAISDYLGANGKGLMLNVTDPASIESVLEKIRAEFGEVDILVNNAGI 89
>pdb|1F1M|A Chain A, Crystal Structure Of Outer Surface Protein C (Ospc)
pdb|1F1M|B Chain B, Crystal Structure Of Outer Surface Protein C (Ospc)
pdb|1F1M|C Chain C, Crystal Structure Of Outer Surface Protein C (Ospc)
pdb|1F1M|D Chain D, Crystal Structure Of Outer Surface Protein C (Ospc)
Length = 164
Score = 26.2 bits (56), Expect = 2.1
Identities = 24/99 (24%), Positives = 42/99 (42%), Gaps = 5/99 (5%)
Query: 69 SLEKSAKEDSSLKTTLSHLYNQLQEIQKSMDKERDYLEEKIITLENKFKDMGHYAASDEI 128
SL A S+L T E++ ++K + EE L+ + D+G +D+
Sbjct: 58 SLMSGAYLISTLITKKISAIKDSGELKAEIEKAKKCSEEFTAKLKGEHTDLGKEGVTDDN 117
Query: 129 NEKQVLKMYQE-GYSVDSISKEFK----VSKGEVEFILN 162
+K +LK + D + K F+ +SK E + N
Sbjct: 118 AKKAILKTNNDKTKGADELEKLFESVKNLSKAAKEMLTN 156
>pdb|1M6N|A Chain A, Crystal Structure Of The Seca Translocation Atpase From
Bacillus Subtilis
pdb|1M74|A Chain A, Crystal Structure Of Mg-Adp-Bound Seca From Bacillus
Subtilis
Length = 802
Score = 25.8 bits (55), Expect = 2.7
Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 6/83 (7%)
Query: 29 KEKEFYHKMRRLEKTLDESYQENYIYSKRLKELEGRLEGLSLEKSAKEDSSL----KTTL 84
K + Y + +TL +++Y Y + K ++ EG++ + A +L L
Sbjct: 229 KSTKLYVQANAFVRTLKA--EKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVAL 286
Query: 85 SHLYNQLQEIQKSMDKERDYLEE 107
+H NQ + +M K+ DY+ E
Sbjct: 287 NHHINQALKAHVAMQKDVDYVVE 309
>pdb|1QHH|B Chain B, Structure Of Dna Helicase With Adpnp
Length = 273
Score = 25.4 bits (54), Expect = 3.5
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 93 EIQKSMDKERDYLEEKIITLENKFKDMGH-YAASDEINEKQV 133
+IQ + ERDY K+I LE ++ A++E+ E V
Sbjct: 96 DIQNILSFERDYPNAKVILLEQNYRSTKRILQAANEVIEHNV 137
>pdb|3PJR|A Chain A, Helicase Substrate Complex
pdb|1PJR| Structure Of Dna Helicase
pdb|1QHG|A Chain A, Structure Of Dna Helicase Mutant With Adpnp
Length = 724
Score = 25.4 bits (54), Expect = 3.5
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 93 EIQKSMDKERDYLEEKIITLENKFKDMGH-YAASDEINEKQV 133
+IQ + ERDY K+I LE ++ A++E+ E V
Sbjct: 263 DIQNILSFERDYPNAKVILLEQNYRSTKRILQAANEVIEHNV 304
>pdb|2PJR|F Chain F, Helicase Product Complex
pdb|2PJR|A Chain A, Helicase Product Complex
Length = 548
Score = 25.4 bits (54), Expect = 3.5
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 93 EIQKSMDKERDYLEEKIITLENKFKDMGH-YAASDEINEKQV 133
+IQ + ERDY K+I LE ++ A++E+ E V
Sbjct: 263 DIQNILSFERDYPNAKVILLEQNYRSTKRILQAANEVIEHNV 304
>pdb|1K3E|B Chain B, Type Iii Secretion Chaperone Cest
pdb|1K3E|A Chain A, Type Iii Secretion Chaperone Cest
Length = 156
Score = 25.0 bits (53), Expect = 4.6
Identities = 14/44 (31%), Positives = 24/44 (53%)
Query: 83 TLSHLYNQLQEIQKSMDKERDYLEEKIITLENKFKDMGHYAASD 126
T L N+++ + KSM+ L + ITLEN+ + ++SD
Sbjct: 105 TPEKLENEIEVVVKSMENLYLVLHNQGITLENEHMKIEEISSSD 148
>pdb|1GTM|A Chain A, Structure Of Glutamate Dehydrogenase
pdb|1GTM|B Chain B, Structure Of Glutamate Dehydrogenase
pdb|1GTM|C Chain C, Structure Of Glutamate Dehydrogenase
Length = 419
Score = 25.0 bits (53), Expect = 4.6
Identities = 11/42 (26%), Positives = 23/42 (54%)
Query: 120 GHYAASDEINEKQVLKMYQEGYSVDSISKEFKVSKGEVEFIL 161
G+Y +E+ E+ KM + Y V +I+KE + + +++
Sbjct: 361 GYYWTIEEVRERLDKKMTKAFYDVYNIAKEKNIHMRDAAYVV 402
>pdb|1MU2|B Chain B, Crystal Structure Of Hiv-2 Reverse Transcriptase
Length = 426
Score = 24.6 bits (52), Expect = 6.0
Identities = 18/72 (25%), Positives = 31/72 (43%), Gaps = 3/72 (4%)
Query: 86 HLYNQLQEIQKSMDKERDYLEEKIITLENKFKDMGHYAASDEINEKQVLKMYQEGYSVDS 145
H Y + +E++ ++ K++D I E K +G YA + + + Q V
Sbjct: 312 HYYQEEKELEATVQKDQDNQWTYKIHQEEKILKVGKYAKVKNTHTNGIRLLAQ---VVQK 368
Query: 146 ISKEFKVSKGEV 157
I KE V G +
Sbjct: 369 IGKEALVIWGRI 380
>pdb|1MU2|A Chain A, Crystal Structure Of Hiv-2 Reverse Transcriptase
Length = 555
Score = 24.6 bits (52), Expect = 6.0
Identities = 18/72 (25%), Positives = 31/72 (43%), Gaps = 3/72 (4%)
Query: 86 HLYNQLQEIQKSMDKERDYLEEKIITLENKFKDMGHYAASDEINEKQVLKMYQEGYSVDS 145
H Y + +E++ ++ K++D I E K +G YA + + + Q V
Sbjct: 317 HYYQEEKELEATVQKDQDNQWTYKIHQEEKILKVGKYAKVKNTHTNGIRLLAQ---VVQK 373
Query: 146 ISKEFKVSKGEV 157
I KE V G +
Sbjct: 374 IGKEALVIWGRI 385
>pdb|1GE9|A Chain A, Solution Structure Of The Ribosome Recycling Factor
Length = 184
Score = 24.3 bits (51), Expect = 7.8
Identities = 15/74 (20%), Positives = 34/74 (45%)
Query: 28 LKEKEFYHKMRRLEKTLDESYQENYIYSKRLKELEGRLEGLSLEKSAKEDSSLKTTLSHL 87
L E+ +R L K +E+ + KE+ LEG+S ++ + L+
Sbjct: 107 LTEERRRELVRLLHKITEEARVRVRNVRREAKEMIEELEGISEDEKKRALERLQKLTDKY 166
Query: 88 YNQLQEIQKSMDKE 101
+++ ++ ++ +KE
Sbjct: 167 IDEINKLMEAKEKE 180
>pdb|1K9X|A Chain A, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Yb
pdb|1K9X|B Chain B, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Yb
pdb|1K9X|C Chain C, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Yb
pdb|1K9X|D Chain D, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Yb
pdb|1KA2|A Chain A, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Mg
pdb|1KA4|A Chain A, Structure Of Pyrococcus Furiosus Carboxypeptidase Nat-Pb
Length = 499
Score = 24.3 bits (51), Expect = 7.8
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 107 EKIITLENKFKDMGHYAASDEINEKQVLKMYQEGYSVDSISKEFKVSKGEVEFILN 162
+KII+L K Y +E +L +Y+EG + K F+V + +++ +L+
Sbjct: 136 DKIISLA---KRAAEYLGYEEEPYDALLDLYEEGLRTRDVEKMFEVLEKKLKPLLD 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
0.315 0.133 0.355
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 861,612
Number of Sequences: 13198
Number of extensions: 33966
Number of successful extensions: 95
Number of sequences better than 10.0: 18
Number of HSP's better than 10.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 83
Number of HSP's gapped (non-prelim): 20
length of query: 168
length of database: 2,899,336
effective HSP length: 82
effective length of query: 86
effective length of database: 1,817,100
effective search space: 156270600
effective search space used: 156270600
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 bits)