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|15644852|ref|NP_207022.1| peptide methionine
sulfoxide reductase (msrA) [Helicobacter pylori 26695]
(359 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|1L1D|B Chain B, Crystal Structure Of The C-Terminal Met... 177 1e-45
pdb|1FVG|A Chain A, Crystal Structure Of Bovine Peptide Met... 102 7e-23
pdb|1FVA|B Chain B, Crystal Structure Of Bovine Methionine ... 102 9e-23
pdb|1FF3|A Chain A, Structure Of The Peptide Methionine Sul... 97 4e-21
pdb|1GAJ|A Chain A, Crystal Structure Of A Nucleotide-Free ... 30 0.42
pdb|1E3D|B Chain B, [nife] Hydrogenase From Desulfovibrio D... 30 0.42
pdb|1G6H|A Chain A, Crystal Structure Of The Adp Conformati... 30 0.42
pdb|1L9M|A Chain A, Three-Dimensional Structure Of The Huma... 29 0.95
pdb|1A0C|A Chain A, Xylose Isomerase From Thermoanaerobacte... 28 1.2
pdb|1M0S|A Chain A, Northeast Structural Genomics Consortiu... 27 2.8
pdb|1KQF|A Chain A, Formate Dehydrogenase N From E. Coli >g... 27 3.6
pdb|1RFN|A Chain A, Human Coagulation Factor Ixa In Complex... 27 4.7
pdb|1ATK| Crystal Structure Of The Cysteine Protease Huma... 26 6.1
pdb|1BY8|A Chain A, The Crystal Structure Of Human Procathe... 26 6.1
>pdb|1L1D|B Chain B, Crystal Structure Of The C-Terminal Methionine Sulfoxide
Reductase Domain (Msrb) Of N. Gonorrhoeae Pilb
pdb|1L1D|A Chain A, Crystal Structure Of The C-Terminal Methionine Sulfoxide
Reductase Domain (Msrb) Of N. Gonorrhoeae Pilb
Length = 152
Score = 177 bits (450), Expect = 1e-45
Identities = 87/150 (58%), Positives = 107/150 (71%), Gaps = 5/150 (3%)
Query: 201 YTKPSDEVLKKKLTKLQYEVTQNKHTEKPFENEYYNKEEEGIYVDITTGEPLFSSADKYD 260
Y KPSD LK+ LT+ QY+VTQN TE F +EY + + GIYVD+ +GEPLFSSADKYD
Sbjct: 8 YKKPSDAELKRTLTEEQYQVTQNSATEYAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYD 67
Query: 261 SGCGWPSFSKPINKDVVKYEDDESLNRKRIEVLSRIGKAHLGHVFNDGPKELGGLRYCIN 320
SGCGWPSF++PI+ V DD S N +R EV SR +HLGHVF DGP++ GGLRYCIN
Sbjct: 68 SGCGWPSFTRPIDAKSVTEHDDFSFNXRRTEVRSRAADSHLGHVFPDGPRDKGGLRYCIN 127
Query: 321 SAALRFIPLKDMEKEGYGEFIPYIKKGELK 350
A+L+FIPL+ + GYG KGE+K
Sbjct: 128 GASLKFIPLEQXDAAGYGAL-----KGEVK 152
>pdb|1FVG|A Chain A, Crystal Structure Of Bovine Peptide Methionine Sulfoxide
Reductase
Length = 199
Score = 102 bits (254), Expect = 7e-23
Identities = 55/149 (36%), Positives = 84/149 (55%), Gaps = 8/149 (5%)
Query: 43 GCFWGLEAYMERIYGVIDASSGYANGKTSSTNYEKL--HESDHAESVKVIYDPKKISLDK 100
GCFWG E + GV G+A G T + Y+++ ++ HAE V+V++ P+ IS ++
Sbjct: 51 GCFWGAERKFWTLKGVYSTQVGFAGGYTPNPTYKEVCSGKTGHAEVVRVVFQPEHISFEE 110
Query: 101 LLRYYFKVVDPVSVNKQGNDVGRQYRTGIY-----YVNSADKEVIDHALKALQKEVKGKI 155
LL+ +++ DP +QGND G QYR+ IY +V +A K D+ K L + G I
Sbjct: 111 LLKVFWENHDPTQGXRQGNDHGSQYRSAIYPTSAEHVGAALKSKEDYQ-KVLSEHGFGLI 169
Query: 156 AIEVEPLKNYVRAEEYHQDYLKKHPSGYC 184
++ + + AE+YHQ YL K P GYC
Sbjct: 170 TTDIREGQTFYYAEDYHQQYLSKDPDGYC 198
>pdb|1FVA|B Chain B, Crystal Structure Of Bovine Methionine Sulfoxide Reductase
pdb|1FVA|A Chain A, Crystal Structure Of Bovine Methionine Sulfoxide Reductase
Length = 217
Score = 102 bits (253), Expect = 9e-23
Identities = 55/149 (36%), Positives = 84/149 (55%), Gaps = 8/149 (5%)
Query: 43 GCFWGLEAYMERIYGVIDASSGYANGKTSSTNYEKL--HESDHAESVKVIYDPKKISLDK 100
GCFWG E + GV G+A G T + Y+++ ++ HAE V+V++ P+ IS ++
Sbjct: 59 GCFWGAERKFWTLKGVYSTQVGFAGGYTPNPTYKEVCSGKTGHAEVVRVVFQPEHISFEE 118
Query: 101 LLRYYFKVVDPVSVNKQGNDVGRQYRTGIY-----YVNSADKEVIDHALKALQKEVKGKI 155
LL+ +++ DP +QGND G QYR+ IY +V +A K D+ K L + G I
Sbjct: 119 LLKVFWENHDPTQGMRQGNDHGSQYRSAIYPTSAEHVGAALKSKEDYQ-KVLSEHGFGLI 177
Query: 156 AIEVEPLKNYVRAEEYHQDYLKKHPSGYC 184
++ + + AE+YHQ YL K P GYC
Sbjct: 178 TTDIREGQTFYYAEDYHQQYLSKDPDGYC 206
>pdb|1FF3|A Chain A, Structure Of The Peptide Methionine Sulfoxide Reductase
From Escherichia Coli
pdb|1FF3|B Chain B, Structure Of The Peptide Methionine Sulfoxide Reductase
From Escherichia Coli
pdb|1FF3|C Chain C, Structure Of The Peptide Methionine Sulfoxide Reductase
From Escherichia Coli
Length = 211
Score = 96.7 bits (239), Expect = 4e-21
Identities = 53/157 (33%), Positives = 82/157 (51%), Gaps = 7/157 (4%)
Query: 37 VIYLAGGCFWGLEAYMERIYGVIDASSGYANGKTSSTNYEKLHESD--HAESVKVIYDPK 94
+ A G FWG+E ++ GV ++GY G T + Y ++ D HAE+V+++YDP
Sbjct: 44 IAIFAMGXFWGVERLFWQLPGVYSTAAGYTGGYTPNPTYREVCSGDTGHAEAVRIVYDPS 103
Query: 95 KISLDKLLRYYFKVVDPVSVNKQGNDVGRQYRTGIYYVNSADKEVIDHALKALQKEVKG- 153
IS ++LL+ +++ DP +QGND G QYR+ IY + +L+ Q +
Sbjct: 104 VISYEQLLQVFWENHDPAQGMRQGNDHGTQYRSAIYPLTPEQDAAARASLERFQAAMLAA 163
Query: 154 ----KIAIEVEPLKNYVRAEEYHQDYLKKHPSGYCHI 186
I E+ + AE+ HQ YL K+P GYC I
Sbjct: 164 DDDRHITTEIANATPFYYAEDDHQQYLHKNPYGYCGI 200
>pdb|1GAJ|A Chain A, Crystal Structure Of A Nucleotide-Free Atp-Binding
Cassette From An Abc Transporter
Length = 257
Score = 30.0 bits (66), Expect = 0.42
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 99 DKLLRYY--FKVVDPVSVNKQGNDVGRQYRTGIYYVNSADKEVIDHALKALQKEVKGKIA 156
+ +++Y+ FK +D VS++ DV T I N + K + + + K +G++
Sbjct: 11 ENIVKYFGEFKALDGVSISVNKGDV-----TLIIGPNGSGKSTLINVITGFLKADEGRVY 65
Query: 157 IEVEPLKNYVRAEEYH 172
E + + N AE YH
Sbjct: 66 FENKDITNKEPAELYH 81
>pdb|1E3D|B Chain B, [nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc
27774
pdb|1E3D|D Chain D, [nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc
27774
Length = 542
Score = 30.0 bits (66), Expect = 0.42
Identities = 27/116 (23%), Positives = 47/116 (40%), Gaps = 14/116 (12%)
Query: 142 HAL---KALQKEVKGKIAIEVEPLKNYVRAEEYHQDYLKK--HPSGYCHIDLKKADEVIV 196
HAL + L+ + I ++N V ++ D+L H +D+ A ++
Sbjct: 78 HALASTRCLEDAINKPIPANATYIRNLVLGNQFMHDHLVHFYHLHALDFVDVTSA--LLA 135
Query: 197 DDDKYTKPSDEVLKKKLTKLQYEVTQNKHTE-------KPFENEYYNKEEEGIYVD 245
D K K ++ + +K T ++ Q K PF N Y+ EG Y+D
Sbjct: 136 DPAKAAKLANSISPRKATTEEFAAVQAKLKTFVASGQLGPFTNAYFLGGHEGYYMD 191
>pdb|1G6H|A Chain A, Crystal Structure Of The Adp Conformation Of Mj1267, An
Atp- Binding Cassette Of An Abc Transporter
Length = 257
Score = 30.0 bits (66), Expect = 0.42
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 99 DKLLRYY--FKVVDPVSVNKQGNDVGRQYRTGIYYVNSADKEVIDHALKALQKEVKGKIA 156
+ +++Y+ FK +D VS++ DV T I N + K + + + K +G++
Sbjct: 11 ENIVKYFGEFKALDGVSISVNKGDV-----TLIIGPNGSGKSTLINVITGFLKADEGRVY 65
Query: 157 IEVEPLKNYVRAEEYH 172
E + + N AE YH
Sbjct: 66 FENKDITNKEPAELYH 81
>pdb|1L9M|A Chain A, Three-Dimensional Structure Of The Human Transglutaminase
3 Enzyme: Binding Of Calcium Ions Change Structure For
Activation
pdb|1L9M|B Chain B, Three-Dimensional Structure Of The Human Transglutaminase
3 Enzyme: Binding Of Calcium Ions Change Structure For
Activation
pdb|1L9N|A Chain A, Three-Dimensional Structure Of The Human Transglutaminase
3 Enzyme: Binding Of Calcium Ions Change Structure For
Activation
pdb|1L9N|B Chain B, Three-Dimensional Structure Of The Human Transglutaminase
3 Enzyme: Binding Of Calcium Ions Change Structure For
Activation
Length = 692
Score = 28.9 bits (63), Expect = 0.95
Identities = 13/28 (46%), Positives = 16/28 (56%)
Query: 73 TNYEKLHESDHAESVKVIYDPKKISLDK 100
TN+ H++D SV V YDP LDK
Sbjct: 294 TNFNSAHDTDRNLSVDVYYDPMGNPLDK 321
>pdb|1A0C|A Chain A, Xylose Isomerase From Thermoanaerobacterium
Thermosulfurigenes
pdb|1A0C|B Chain B, Xylose Isomerase From Thermoanaerobacterium
Thermosulfurigenes
pdb|1A0C|C Chain C, Xylose Isomerase From Thermoanaerobacterium
Thermosulfurigenes
pdb|1A0C|D Chain D, Xylose Isomerase From Thermoanaerobacterium
Thermosulfurigenes
Length = 438
Score = 28.5 bits (62), Expect = 1.2
Identities = 15/45 (33%), Positives = 27/45 (59%), Gaps = 1/45 (2%)
Query: 215 KLQYEVTQNKHTEKPFENEYYNKEEEGIYVDITTGEPLFSSADKY 259
K+ Y++ +++ +K F E Y ++GI DI +G+ F S +KY
Sbjct: 367 KVAYKLVKDRVFDK-FIEERYASYKDGIGADIVSGKADFRSLEKY 410
>pdb|1M0S|A Chain A, Northeast Structural Genomics Consortium (Nesg Id Ir21)
pdb|1M0S|B Chain B, Northeast Structural Genomics Consortium (Nesg Id Ir21)
Length = 219
Score = 27.3 bits (59), Expect = 2.8
Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 89 VIYDPKKISLDKLLRYYFKVVDPVSVNKQGNDVGRQYRTGIYYVNSADKEVI 140
V+ D + LD + F +++PV + K+ N+V GI+ + AD ++
Sbjct: 161 VVTDNGNVILDV---HNFSILNPVEIEKELNNVAGVVTNGIFALRGADVVIV 209
>pdb|1KQF|A Chain A, Formate Dehydrogenase N From E. Coli
pdb|1KQG|A Chain A, Formate Dehydrogenase N From E. Coli
Length = 1015
Score = 26.9 bits (58), Expect = 3.6
Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 140 IDHALKALQKEVKGKIAIEVEPLK----NYVRAEEYHQDYLKKHPSGYCHIDLKKADEVI 195
I H L+ L + GK VEPL NY + E D + K +GY DL A+ V+
Sbjct: 656 IYHHLRELYQSEGGK---GVEPLMKMSWNYKQPHEPQSDEVAKENNGYALEDLYDANGVL 712
Query: 196 V 196
+
Sbjct: 713 I 713
>pdb|1RFN|A Chain A, Human Coagulation Factor Ixa In Complex With P-Amino
Benzamidine
Length = 235
Score = 26.6 bits (57), Expect = 4.7
Identities = 14/41 (34%), Positives = 17/41 (41%)
Query: 27 GSQHQKTDERVIYLAGGCFWGLEAYMERIYGVIDASSGYAN 67
G H E +L G WG E M+ YG+ S Y N
Sbjct: 186 GGPHVTEVEGTSFLTGIISWGEECAMKGKYGIYTKVSRYVN 226
>pdb|1ATK| Crystal Structure Of The Cysteine Protease Human Cathepsin K In
Complex With The Covalent Inhibitor E-64
pdb|1AYU| Crystal Structure Of Cysteine Protease Human Cathepsin K In
Complex With A Covalent Symmetric Biscarbohydrazide
Inhibitor
pdb|1AU4| Crystal Structure Of The Cysteine Protease Human Cathepsin K In
Complex With A Covalent Pyrrolidinone Inhibitor
pdb|1AYV| Crystal Structure Of Cysteine Protease Human Cathepsin K In
Complex With A Covalent Thiazolhydrazide Inhibitor
pdb|1BGO| Crystal Structure Of Cysteine Protease Human Cathepsin K In
Complex With A Covalent Peptidomimetic Inhibitor
pdb|1AYW| Crystal Structure Of Cysteine Protease Human Cathepsin K In
Complex With A Covalent Benzyloxybenzoylcarbohydrazide
Inhibitor
pdb|1AU3| Crystal Structure Of The Cysteine Protease Human Cathepsin K In
Complex With A Covalent Pyrrolidinone Inhibitor
pdb|1AU0| Crystal Structure Of The Cysteine Protease Human Cathepsin K In
Complex With A Covalent Symmetric Diacylaminomethyl
Ketone Inhibitor
pdb|1AU2| Crystal Structure Of The Cysteine Protease Human Cathepsin K In
Complex With A Covalent Propanone Inhibitor
pdb|1MEM|A Chain A, Crystal Structure Of Cathepsin K Complexed With A Potent
Vinyl Sulfone Inhibitor
Length = 215
Score = 26.2 bits (56), Expect = 6.1
Identities = 27/108 (25%), Positives = 46/108 (42%), Gaps = 7/108 (6%)
Query: 42 GGCFWGLEAYMERIYGVIDASSGYAN-GKTSSTNYEKLHESDHAESVKVIYDPKKISLDK 100
GG Y+++ G ID+ Y G+ S Y ++ + I + +K
Sbjct: 65 GGYMTNAFQYVQKNRG-IDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGN----EK 119
Query: 101 LLRYYFKVVDPVSVNKQGNDVGRQ-YRTGIYYVNSADKEVIDHALKAL 147
L+ V PVSV + Q Y G+YY S + + ++HA+ A+
Sbjct: 120 ALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAV 167
>pdb|1BY8|A Chain A, The Crystal Structure Of Human Procathepsin K
pdb|7PCK|A Chain A, Crystal Structure Of Wild Type Human Procathepsin K
pdb|7PCK|B Chain B, Crystal Structure Of Wild Type Human Procathepsin K
pdb|7PCK|C Chain C, Crystal Structure Of Wild Type Human Procathepsin K
pdb|7PCK|D Chain D, Crystal Structure Of Wild Type Human Procathepsin K
Length = 314
Score = 26.2 bits (56), Expect = 6.1
Identities = 27/108 (25%), Positives = 46/108 (42%), Gaps = 7/108 (6%)
Query: 42 GGCFWGLEAYMERIYGVIDASSGYAN-GKTSSTNYEKLHESDHAESVKVIYDPKKISLDK 100
GG Y+++ G ID+ Y G+ S Y ++ + I + +K
Sbjct: 164 GGYMTNAFQYVQKNRG-IDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGN----EK 218
Query: 101 LLRYYFKVVDPVSVNKQGNDVGRQ-YRTGIYYVNSADKEVIDHALKAL 147
L+ V PVSV + Q Y G+YY S + + ++HA+ A+
Sbjct: 219 ALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAV 266
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
0.314 0.136 0.392
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,249,565
Number of Sequences: 13198
Number of extensions: 100678
Number of successful extensions: 193
Number of sequences better than 10.0: 14
Number of HSP's better than 10.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 180
Number of HSP's gapped (non-prelim): 14
length of query: 359
length of database: 2,899,336
effective HSP length: 89
effective length of query: 270
effective length of database: 1,724,714
effective search space: 465672780
effective search space used: 465672780
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (25.8 bits)