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|15644721|ref|NP_206891.1| type II restriction enzyme
R protein (hsdR) [Helicobacter pylori 26695]
(277 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|1CQG|A Chain A, High Resolution Solution Nmr Structure ... 32 0.080
pdb|1TRS| Thioredoxin Mutant With Cys 62 Replaced By Ala,... 32 0.080
pdb|1AIU| Human Thioredoxin (D60n Mutant, Reduced Form) 31 0.18
pdb|1ERW| Human Thioredoxin Double Mutant With Cys 32 Rep... 30 0.23
pdb|1ERT| Human Thioredoxin (Reduced Form) >gi|2982059|pd... 30 0.30
pdb|1ERV| Human Thioredoxin Mutant With Cys 73 Replaced B... 30 0.30
pdb|3TRX| Thioredoxin (Reduced Form) >gi|231098|pdb|4TRX|... 30 0.40
pdb|1KCW| X-Ray Crystal Structure Of Human Ceruloplasmin ... 28 1.2
pdb|1EZT|A Chain A, High-Resolution Solution Structure Of F... 27 3.4
pdb|1AGR|E Chain E, Complex Of Alf4-Activated Gi-Alpha-1 Wi... 27 3.4
pdb|1DQ3|A Chain A, Crystal Structure Of An Archaeal Intein... 26 5.7
pdb|1G8X|A Chain A, Structure Of A Genetically Engineered M... 25 9.8
pdb|1MMG| X-Ray Structures Of The Mgadp, Mgatpgammas, And... 25 9.8
pdb|1LVK| X-Ray Crystal Structure Of The Mg (Dot) 2'(3')-... 25 9.8
pdb|1DMT|A Chain A, Structure Of Human Neutral Endopeptidas... 25 9.8
pdb|1MMN| X-Ray Structures Of The Mgadp, Mgatpgammas, And... 25 9.8
>pdb|1CQG|A Chain A, High Resolution Solution Nmr Structure Of Mixed Disulfide
Intermediate Between Human Thioredoxin (C35a, C62a,
C69a, C73a) Mutant And A 13 Residue Peptide Comprising
Its Target Site In Human Ref-1 (Residues 59 - 71 Of The
P50 Subunit Of Nfkb), Nmr, 31 Structures
pdb|1CQH|A Chain A, High Resolution Solution Nmr Structure Of Mixed Disulfide
Intermediate Between Human Thioredoxin (C35a, C62a,
C69a, C73a) Mutant And A 13 Residue Peptide Comprising
Its Target Site In Human Ref-1 (Residues 59 - 71 Of The
P50 Subunit Of Nfkb), Nmr, Minimized Average Structure
pdb|1MDI|A Chain A, High Resolution Solution Nmr Structure Of Mixed Disulfide
Intermediate Between Mutant Human Thioredoxin And A 13
Residue Peptide Comprising Its Target Site In Human Nfkb
pdb|1MDJ|A Chain A, High Resolution Solution Nmr Structure Of Mixed Disulfide
Intermediate Between Human Thioredoxin (C35a, C62a,
C69a, C73a) Mutant And A 13 Residue Peptide Comprising
Its Target Site In Human Nfkb (Residues 56-68 Of The P50
Subunit Of Nfkb)
pdb|1MDK|A Chain A, High Resolution Solution Nmr Structure Of Mixed Disulfide
Intermediate Between Human Thioredoxin (C35a, C62a,
C69a, C73a) Mutant And A 13 Residue Peptide Comprising
Its Target Site In Human Nfkb (Residues 56-68 Of The P50
Subunit Of Nfkb)
Length = 105
Score = 32.0 bits (71), Expect = 0.080
Identities = 18/57 (31%), Positives = 31/57 (53%), Gaps = 3/57 (5%)
Query: 53 KELKNCIKSLFKEYPKAFNVLNILIAVRDKKDIVLDANGNFYPLYSYFEDGEKVYEF 109
K +K SL ++Y NV+ + + V D +D+ +A P + +F+ G+KV EF
Sbjct: 36 KMIKPFFHSLSEKYS---NVIFLEVDVDDAQDVASEAEVKATPTFQFFKKGQKVGEF 89
>pdb|1TRS| Thioredoxin Mutant With Cys 62 Replaced By Ala, Cys 69 Replaced By
Ala, Cys 73 Replaced By Ala (C62a,C69a,C73a) (Oxidized)
(Nmr, Minimized Average Structure)
pdb|1TRU| Thioredoxin Mutant With Cys 62 Replaced By Ala, Cys 69 Replaced By
Ala, Cys 73 Replaced By Ala (C62a,C69a,C73a) (Oxidized)
(Nmr, 40 Structures)
pdb|1TRV| Thioredoxin Mutant With Cys 62 Replaced By Ala, Cys 69 Replaced By
Ala, Cys 73 Replaced By Ala (C62a,C69a,C73a) (Reduced)
(Nmr, 40 Structures)
pdb|1TRW| Thioredoxin Mutant With Cys 62 Replaced By Ala, Cys 69 Replaced By
Ala, Cys 73 Replaced By Ala (C62a,C69a,C73a) (Reduced)
(Nmr, Minimized Average Structure)
Length = 105
Score = 32.0 bits (71), Expect = 0.080
Identities = 18/57 (31%), Positives = 31/57 (53%), Gaps = 3/57 (5%)
Query: 53 KELKNCIKSLFKEYPKAFNVLNILIAVRDKKDIVLDANGNFYPLYSYFEDGEKVYEF 109
K +K SL ++Y NV+ + + V D +D+ +A P + +F+ G+KV EF
Sbjct: 36 KMIKPFFHSLSEKYS---NVIFLEVDVDDAQDVASEAEVKATPTFQFFKKGQKVGEF 89
>pdb|1AIU| Human Thioredoxin (D60n Mutant, Reduced Form)
Length = 105
Score = 30.8 bits (68), Expect = 0.18
Identities = 17/57 (29%), Positives = 30/57 (51%), Gaps = 3/57 (5%)
Query: 53 KELKNCIKSLFKEYPKAFNVLNILIAVRDKKDIVLDANGNFYPLYSYFEDGEKVYEF 109
K +K SL ++Y NV+ + + V D +D+ + P + +F+ G+KV EF
Sbjct: 36 KMIKPFFHSLSEKYS---NVIFLEVDVNDCQDVASECEVKCMPTFQFFKKGQKVGEF 89
>pdb|1ERW| Human Thioredoxin Double Mutant With Cys 32 Replaced By Ser And
Cys 35 Replaced By Ser
Length = 105
Score = 30.4 bits (67), Expect = 0.23
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 52 TKELKNCIKSLFKEYPKAFNVLNILIAVRDKKDIVLDANGNFYPLYSYFEDGEKVYEF 109
+K +K SL ++Y NV+ + + V D +D+ + P + +F+ G+KV EF
Sbjct: 35 SKMIKPFFHSLSEKYS---NVIFLEVDVDDCQDVASECEVKCMPTFQFFKKGQKVGEF 89
>pdb|1ERT| Human Thioredoxin (Reduced Form)
pdb|1AUC| Human Thioredoxin (Oxidized With Diamide)
pdb|1ERU| Human Thioredoxin (Oxidized Form)
Length = 105
Score = 30.0 bits (66), Expect = 0.30
Identities = 17/57 (29%), Positives = 30/57 (51%), Gaps = 3/57 (5%)
Query: 53 KELKNCIKSLFKEYPKAFNVLNILIAVRDKKDIVLDANGNFYPLYSYFEDGEKVYEF 109
K +K SL ++Y NV+ + + V D +D+ + P + +F+ G+KV EF
Sbjct: 36 KMIKPFFHSLSEKYS---NVIFLEVDVDDCQDVASECEVKCMPTFQFFKKGQKVGEF 89
>pdb|1ERV| Human Thioredoxin Mutant With Cys 73 Replaced By Ser (Reduced
Form)
Length = 105
Score = 30.0 bits (66), Expect = 0.30
Identities = 17/57 (29%), Positives = 30/57 (51%), Gaps = 3/57 (5%)
Query: 53 KELKNCIKSLFKEYPKAFNVLNILIAVRDKKDIVLDANGNFYPLYSYFEDGEKVYEF 109
K +K SL ++Y NV+ + + V D +D+ + P + +F+ G+KV EF
Sbjct: 36 KMIKPFFHSLSEKYS---NVIFLEVDVDDCQDVASECEVKSMPTFQFFKKGQKVGEF 89
>pdb|3TRX| Thioredoxin (Reduced Form)
pdb|4TRX| Thioredoxin (Reduced Form)
Length = 105
Score = 29.6 bits (65), Expect = 0.40
Identities = 17/57 (29%), Positives = 30/57 (51%), Gaps = 3/57 (5%)
Query: 53 KELKNCIKSLFKEYPKAFNVLNILIAVRDKKDIVLDANGNFYPLYSYFEDGEKVYEF 109
K +K SL ++Y NV+ + + V D +D+ + P + +F+ G+KV EF
Sbjct: 36 KMIKPFFHSLSEKYS---NVIFLEVDVDDCQDVASECEVKCTPTFQFFKKGQKVGEF 89
>pdb|1KCW| X-Ray Crystal Structure Of Human Ceruloplasmin At 3.0 Angstroms
Length = 1046
Score = 28.1 bits (61), Expect = 1.2
Identities = 21/84 (25%), Positives = 32/84 (38%), Gaps = 2/84 (2%)
Query: 184 DDIKKFDFVVCGKDKTYFIEANFYTISGSKLNEVARSYQDLAL--KFEAFPNYEFIWITD 241
D K + G D F E I GS V R Y D + + E P E + I
Sbjct: 372 DIFTKENLTAPGSDSAVFFEQGTTRIGGSYKKLVYREYTDASFTNRKERGPEEEHLGILG 431
Query: 242 GIGWLDAKNKLQEAYKSVEIYNLS 265
+ W + + ++ + + Y LS
Sbjct: 432 PVIWAEVGDTIRVTFHNKGAYPLS 455
>pdb|1EZT|A Chain A, High-Resolution Solution Structure Of Free Rgs4 By Nmr
pdb|1EZY|A Chain A, High-Resolution Solution Structure Of Free Rgs4 By Nmr
Length = 166
Score = 26.6 bits (57), Expect = 3.4
Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 8/79 (10%)
Query: 59 IKSLFKEYPKAFNVLNILIAVRDKKDIVLD-------ANGNFYPLYSYFEDGE-KVYEFI 110
IKS K PKA + N I+V+ K++ LD + P + F++ + K++ +
Sbjct: 55 IKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLM 114
Query: 111 RQTGLERIFCNRNIKDLND 129
+ R +R DL +
Sbjct: 115 EKDSYRRFLKSRFYLDLTN 133
>pdb|1AGR|E Chain E, Complex Of Alf4-Activated Gi-Alpha-1 With Rgs4
pdb|1AGR|H Chain H, Complex Of Alf4-Activated Gi-Alpha-1 With Rgs4
Length = 205
Score = 26.6 bits (57), Expect = 3.4
Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 8/79 (10%)
Query: 59 IKSLFKEYPKAFNVLNILIAVRDKKDIVLD-------ANGNFYPLYSYFEDGE-KVYEFI 110
IKS K PKA + N I+V+ K++ LD + P + F++ + K++ +
Sbjct: 101 IKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLM 160
Query: 111 RQTGLERIFCNRNIKDLND 129
+ R +R DL +
Sbjct: 161 EKDSYRRFLKSRFYLDLTN 179
>pdb|1DQ3|A Chain A, Crystal Structure Of An Archaeal Intein-Encoded Homing
Endonuclease Pi-Pfui
Length = 454
Score = 25.8 bits (55), Expect = 5.7
Identities = 17/83 (20%), Positives = 34/83 (40%), Gaps = 7/83 (8%)
Query: 105 KVYEFIRQTGLERIFCNRNIKDLNDFVFGIEVGLDSNARKNRSGKVMENHLSGLFTNAQL 164
++ E +R+ G++ + L F I L + ++ + KV+ NH G
Sbjct: 284 RIREKLRKDGIDYVLHVEEYSSLLRFYELIGKNLQNEEKREKLEKVLSNHKGG------- 336
Query: 165 NFKEQVEIREFEDLCQAFGDDIK 187
NF + F++ +G + K
Sbjct: 337 NFGLPLNFNAFKEWASEYGVEFK 359
>pdb|1G8X|A Chain A, Structure Of A Genetically Engineered Molecular Motor
pdb|1G8X|B Chain B, Structure Of A Genetically Engineered Molecular Motor
Length = 1010
Score = 25.0 bits (53), Expect = 9.8
Identities = 14/43 (32%), Positives = 25/43 (57%), Gaps = 3/43 (6%)
Query: 186 IKKFDFVVCGKDKTYFIEANFYTISGSKLNEVARSYQDLALKF 228
+KK + V+C + K YFI ISG ++ +V S++ L + +
Sbjct: 434 VKKINNVLCSERKAYFI--GVLDISGFEIFKV-NSFEQLCINY 473
>pdb|1MMG| X-Ray Structures Of The Mgadp, Mgatpgammas, And Mgamppnp Complexes
Of The Dictyostelium Discoideum Myosin Motor Domain
Length = 762
Score = 25.0 bits (53), Expect = 9.8
Identities = 14/43 (32%), Positives = 25/43 (57%), Gaps = 3/43 (6%)
Query: 186 IKKFDFVVCGKDKTYFIEANFYTISGSKLNEVARSYQDLALKF 228
+KK + V+C + K YFI ISG ++ +V S++ L + +
Sbjct: 434 VKKINNVLCSERKAYFI--GVLDISGFEIFKV-NSFEQLCINY 473
>pdb|1LVK| X-Ray Crystal Structure Of The Mg (Dot)
2'(3')-O-(N-Methylanthraniloyl) Nucleotide Bound To
Dictyostelium Discoideum Myosin Motor Domain
Length = 762
Score = 25.0 bits (53), Expect = 9.8
Identities = 14/43 (32%), Positives = 25/43 (57%), Gaps = 3/43 (6%)
Query: 186 IKKFDFVVCGKDKTYFIEANFYTISGSKLNEVARSYQDLALKF 228
+KK + V+C + K YFI ISG ++ +V S++ L + +
Sbjct: 434 VKKINNVLCSERKAYFI--GVLDISGFEIFKV-NSFEQLCINY 473
>pdb|1DMT|A Chain A, Structure Of Human Neutral Endopeptidase Complexed With
Phosphoramidon
Length = 696
Score = 25.0 bits (53), Expect = 9.8
Identities = 20/78 (25%), Positives = 34/78 (42%), Gaps = 10/78 (12%)
Query: 209 ISGSKLNEVARSYQDLALKFEAFPNYE---------FIWITDGIGWLDAKNKLQEAYKSV 259
++G+ N V R Y + A E+ E FI D + W+DA+ K + K++
Sbjct: 361 VNGNMENAVGRLYVEAAFAGESKHVVEDLIAQIREVFIQTLDDLTWMDAETKKRAEEKAL 420
Query: 260 EI-YNLSNVNDFISKAQK 276
I + +D +S K
Sbjct: 421 AIKERIGYPDDIVSNDNK 438
>pdb|1MMN| X-Ray Structures Of The Mgadp, Mgatpgammas, And Mgamppnp Complexes
Of The Dictyostelium Discoideum Myosin Motor Domain
Length = 762
Score = 25.0 bits (53), Expect = 9.8
Identities = 14/43 (32%), Positives = 25/43 (57%), Gaps = 3/43 (6%)
Query: 186 IKKFDFVVCGKDKTYFIEANFYTISGSKLNEVARSYQDLALKF 228
+KK + V+C + K YFI ISG ++ +V S++ L + +
Sbjct: 434 VKKINNVLCSERKAYFI--GVLDISGFEIFKV-NSFEQLCINY 473
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
0.322 0.140 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: 1,642,484
Number of Sequences: 13198
Number of extensions: 70507
Number of successful extensions: 214
Number of sequences better than 10.0: 16
Number of HSP's better than 10.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 207
Number of HSP's gapped (non-prelim): 16
length of query: 277
length of database: 2,899,336
effective HSP length: 87
effective length of query: 190
effective length of database: 1,751,110
effective search space: 332710900
effective search space used: 332710900
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: 53 (25.0 bits)