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|15645229|ref|NP_207399.1| uroporphyrinogen
decarboxylase (hemE) [Helicobacter pylori 26695]
(340 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|1URO|A Chain A, Uroporphyrinogen Decarboxylase 242 4e-65
pdb|1JPH|A Chain A, Ile260thr Mutant Of Human Urod, Human U... 241 9e-65
pdb|1JPI|A Chain A, Phe232leu Mutant Of Human Urod, Human U... 240 2e-64
pdb|1JPK|A Chain A, Gly156asp Mutant Of Human Urod, Human U... 239 3e-64
pdb|1J93|A Chain A, Crystal Structure And Substrate Binding... 215 7e-57
pdb|1EKF|A Chain A, Crystallographic Structure Of Human Bra... 30 0.39
pdb|1M5S|A Chain A, Formylmethanofuran:tetrahydromethanopte... 29 0.67
pdb|1BM8| Dna-Binding Domain Of Mbp1 28 2.0
pdb|1MB1| Mbp1 From Saccharomyces Cerevisiae 28 2.0
pdb|4THI|A Chain A, Thiaminase I From Bacillus Thiaminolyti... 25 9.7
pdb|1JB9|A Chain A, Crystal Structure Of The Ferredoxin:nad... 25 9.7
pdb|2THI|A Chain A, Thiaminase I From Bacillus Thiaminolyti... 25 9.7
pdb|3THI|A Chain A, Thiaminase I From Bacillus Thiaminolyticus 25 9.7
pdb|1KTB|A Chain A, The Structure Of Alpha-N-Acetylgalactos... 25 9.7
>pdb|1URO|A Chain A, Uroporphyrinogen Decarboxylase
Length = 367
Score = 242 bits (618), Expect = 4e-65
Identities = 137/348 (39%), Positives = 206/348 (58%), Gaps = 16/348 (4%)
Query: 4 FIDACFRKETPYTPIWMMRQAGRYLSEYQESRKKAGSFLELCKNSDLATEVTLQPVEILG 63
F+ A + +ET YTP+W MRQAGRYL E++E+R A F C++ + E+TLQP+
Sbjct: 19 FLRAAWGEETDYTPVWCMRQAGRYLPEFRETRA-AQDFFSTCRSPEACCELTLQPLRRFP 77
Query: 64 VDAAILFSDILVVPLEMGLNLEFIPKKGPHFLETITDLKSVESLKVGAY--KQLNYVYDT 121
+DAAI+FSDILVVP +G+ + +P KGP F E + + + +E L+ +L YV+
Sbjct: 78 LDAAIIFSDILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQA 137
Query: 122 ISQTRQKLSREKALIGFCGSPWTLATYMIEGEGSKSYAKSKKMLYSEPEVLKALLEKLSL 181
I+ TRQ+L+ LIGF G+PWTL TYM+EG GS + A++K+ LY P+ LL L+
Sbjct: 138 ITLTRQRLAGRVPLIGFAGAPWTLMTYMVEGGGSSTMAQAKRWLYQRPQASHQLLRILTD 197
Query: 182 ELIEYLSLQIQAGVNAVMIFDSWASALEKEAYLKFSWDYLKKISKELKKR-----YAHIP 236
L+ YL Q+ AG A+ +F+S A L + + KF+ Y++ ++K++K R A +P
Sbjct: 198 ALVPYLVGQVVAGAQALQLFESHAGHLGPQLFNKFALPYIRDVAKQVKARLREAGLAPVP 257
Query: 237 VILFPK-GIGAYLDSIDGEFDVFGVDWGTPLTAAKKILGGKYVLQGNLEPTRLYDKNALE 295
+I+F K G A + ++V G+DW A++ +G LQGNL+P LY A E
Sbjct: 258 MIIFAKDGHFALEELAQAGYEVVGLDWTVAPKKARECVGKTVTLQGNLDPCALY---ASE 314
Query: 296 EGVETILKVM----GNQGHIFNLGHGMLPDLPRENAKYLVQLVHAKTR 339
E + ++K M G +I NLGHG+ PD+ E+ V VH +R
Sbjct: 315 EEIGQLVKQMLDDFGPHRYIANLGHGLYPDMDPEHVGAFVDAVHKHSR 362
>pdb|1JPH|A Chain A, Ile260thr Mutant Of Human Urod, Human Uroporphyrinogen Iii
Decarboxylase
Length = 388
Score = 241 bits (615), Expect = 9e-65
Identities = 137/348 (39%), Positives = 205/348 (58%), Gaps = 16/348 (4%)
Query: 4 FIDACFRKETPYTPIWMMRQAGRYLSEYQESRKKAGSFLELCKNSDLATEVTLQPVEILG 63
F+ A + +ET YTP+W MRQAGRYL E++E+R A F C++ + E+TLQP+
Sbjct: 40 FLRAAWGEETDYTPVWCMRQAGRYLPEFRETRA-AQDFFSTCRSPEACCELTLQPLRRFP 98
Query: 64 VDAAILFSDILVVPLEMGLNLEFIPKKGPHFLETITDLKSVESLKVGAY--KQLNYVYDT 121
+DAAI+FSDILVVP +G+ + +P KGP F E + + + +E L+ +L YV+
Sbjct: 99 LDAAIIFSDILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQA 158
Query: 122 ISQTRQKLSREKALIGFCGSPWTLATYMIEGEGSKSYAKSKKMLYSEPEVLKALLEKLSL 181
I+ TRQ+L+ LIGF G+PWTL TYM+EG GS + A++K+ LY P+ LL L+
Sbjct: 159 ITLTRQRLAGRVPLIGFAGAPWTLMTYMVEGGGSSTMAQAKRWLYQRPQASHQLLRILTD 218
Query: 182 ELIEYLSLQIQAGVNAVMIFDSWASALEKEAYLKFSWDYLKKISKELKKR-----YAHIP 236
L+ YL Q+ AG A+ +F+S A L + + KF+ Y++ ++K++K R A +P
Sbjct: 219 ALVPYLVGQVVAGAQALQLFESHAGHLGPQLFNKFALPYIRDVAKQVKARLREAGLAPVP 278
Query: 237 VILFPK-GIGAYLDSIDGEFDVFGVDWGTPLTAAKKILGGKYVLQGNLEPTRLYDKNALE 295
+I F K G A + ++V G+DW A++ +G LQGNL+P LY A E
Sbjct: 279 MITFAKDGHFALEELAQAGYEVVGLDWTVAPKKARECVGKTVTLQGNLDPCALY---ASE 335
Query: 296 EGVETILKVM----GNQGHIFNLGHGMLPDLPRENAKYLVQLVHAKTR 339
E + ++K M G +I NLGHG+ PD+ E+ V VH +R
Sbjct: 336 EEIGQLVKQMLDDFGPHRYIANLGHGLYPDMDPEHVGAFVDAVHKHSR 383
>pdb|1JPI|A Chain A, Phe232leu Mutant Of Human Urod, Human Uroporphyrinogen Iii
Decarboxylase
Length = 388
Score = 240 bits (612), Expect = 2e-64
Identities = 136/348 (39%), Positives = 205/348 (58%), Gaps = 16/348 (4%)
Query: 4 FIDACFRKETPYTPIWMMRQAGRYLSEYQESRKKAGSFLELCKNSDLATEVTLQPVEILG 63
F+ A + +ET YTP+W MRQAGRYL E++E+R A F C++ + E+TLQP+
Sbjct: 40 FLRAAWGEETDYTPVWCMRQAGRYLPEFRETRA-AQDFFSTCRSPEACCELTLQPLRRFP 98
Query: 64 VDAAILFSDILVVPLEMGLNLEFIPKKGPHFLETITDLKSVESLKVGAY--KQLNYVYDT 121
+DAAI+FSDILVVP +G+ + +P KGP F E + + + +E L+ +L YV+
Sbjct: 99 LDAAIIFSDILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQA 158
Query: 122 ISQTRQKLSREKALIGFCGSPWTLATYMIEGEGSKSYAKSKKMLYSEPEVLKALLEKLSL 181
I+ TRQ+L+ LIGF G+PWTL TYM+EG GS + A++K+ LY P+ LL L+
Sbjct: 159 ITLTRQRLAGRVPLIGFAGAPWTLMTYMVEGGGSSTMAQAKRWLYQRPQASHQLLRILTD 218
Query: 182 ELIEYLSLQIQAGVNAVMIFDSWASALEKEAYLKFSWDYLKKISKELKKR-----YAHIP 236
L+ YL Q+ AG A+ +F+S A L + + K + Y++ ++K++K R A +P
Sbjct: 219 ALVPYLVGQVVAGAQALQLFESHAGHLGPQLFNKLALPYIRDVAKQVKARLREAGLAPVP 278
Query: 237 VILFPK-GIGAYLDSIDGEFDVFGVDWGTPLTAAKKILGGKYVLQGNLEPTRLYDKNALE 295
+I+F K G A + ++V G+DW A++ +G LQGNL+P LY A E
Sbjct: 279 MIIFAKDGHFALEELAQAGYEVVGLDWTVAPKKARECVGKTVTLQGNLDPCALY---ASE 335
Query: 296 EGVETILKVM----GNQGHIFNLGHGMLPDLPRENAKYLVQLVHAKTR 339
E + ++K M G +I NLGHG+ PD+ E+ V VH +R
Sbjct: 336 EEIGQLVKQMLDDFGPHRYIANLGHGLYPDMDPEHVGAFVDAVHKHSR 383
>pdb|1JPK|A Chain A, Gly156asp Mutant Of Human Urod, Human Uroporphyrinogen Iii
Decarboxylase
Length = 388
Score = 239 bits (611), Expect = 3e-64
Identities = 136/348 (39%), Positives = 205/348 (58%), Gaps = 16/348 (4%)
Query: 4 FIDACFRKETPYTPIWMMRQAGRYLSEYQESRKKAGSFLELCKNSDLATEVTLQPVEILG 63
F+ A + +ET YTP+W MRQAGRYL E++E+R A F C++ + E+TLQP+
Sbjct: 40 FLRAAWGEETDYTPVWCMRQAGRYLPEFRETRA-AQDFFSTCRSPEACCELTLQPLRRFP 98
Query: 64 VDAAILFSDILVVPLEMGLNLEFIPKKGPHFLETITDLKSVESLKVGAY--KQLNYVYDT 121
+DAAI+FSDILVVP +G+ + +P KGP F E + + + +E L+ +L YV+
Sbjct: 99 LDAAIIFSDILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQA 158
Query: 122 ISQTRQKLSREKALIGFCGSPWTLATYMIEGEGSKSYAKSKKMLYSEPEVLKALLEKLSL 181
I+ TRQ+L+ LIGF +PWTL TYM+EG GS + A++K+ LY P+ LL L+
Sbjct: 159 ITLTRQRLAGRVPLIGFADAPWTLMTYMVEGGGSSTMAQAKRWLYQRPQASHQLLRILTD 218
Query: 182 ELIEYLSLQIQAGVNAVMIFDSWASALEKEAYLKFSWDYLKKISKELKKR-----YAHIP 236
L+ YL Q+ AG A+ +F+S A L + + KF+ Y++ ++K++K R A +P
Sbjct: 219 ALVPYLVGQVVAGAQALQLFESHAGHLGPQLFNKFALPYIRDVAKQVKARLREAGLAPVP 278
Query: 237 VILFPK-GIGAYLDSIDGEFDVFGVDWGTPLTAAKKILGGKYVLQGNLEPTRLYDKNALE 295
+I+F K G A + ++V G+DW A++ +G LQGNL+P LY A E
Sbjct: 279 MIIFAKDGHFALEELAQAGYEVVGLDWTVAPKKARECVGKTVTLQGNLDPCALY---ASE 335
Query: 296 EGVETILKVM----GNQGHIFNLGHGMLPDLPRENAKYLVQLVHAKTR 339
E + ++K M G +I NLGHG+ PD+ E+ V VH +R
Sbjct: 336 EEIGQLVKQMLDDFGPHRYIANLGHGLYPDMDPEHVGAFVDAVHKHSR 383
>pdb|1J93|A Chain A, Crystal Structure And Substrate Binding Modeling Of The
Uroporphyrinogen-Iii Decarboxylase From Nicotiana
Tabacum: Implications For The Catalytic Mechanism
Length = 353
Score = 215 bits (547), Expect = 7e-57
Identities = 115/334 (34%), Positives = 189/334 (56%), Gaps = 3/334 (0%)
Query: 3 IFIDACFRKETPYTPIWMMRQAGRYLSEYQESRKKAGSFLELCKNSDLATEVTLQPVEIL 62
+ +DA KE P+W+MRQAGRY+ YQ +K F + +N DL E++LQP ++
Sbjct: 14 LLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPWKVF 73
Query: 63 GVDAAILFSDILVVPLEMGLNLEFIPKKGPHFLETITDLKSVESLKVGA-YKQLNYVYDT 121
D ILFSDIL M + + I KGP + + VE ++ K + YV +
Sbjct: 74 RPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYVGEA 133
Query: 122 ISQTRQKLSREKALIGFCGSPWTLATYMIEGEGSKSYAKSKKMLYSEPEVLKALLEKLSL 181
++ R++++ + A++GF G+P+TLA+Y++EG SK++ K K++ ++EP+VL ALL+K +
Sbjct: 134 LTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFAT 193
Query: 182 ELIEYLSLQIQAGVNAVMIFDSWASALEKEAYLKFSWDYLKKISKELKKRYAHIPVILFP 241
+ +Y+ Q +G AV IFDSWA+ L + +FS YLK+I +K + ++P+IL+
Sbjct: 194 SMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYA 253
Query: 242 KGIGAYLDSID-GEFDVFGVDWGTPLTAAKKILGGKYVLQGNLEPTRLY-DKNALEEGVE 299
G G L+ + DV +DW + ++ LG +QGN++P L+ K + +
Sbjct: 254 SGSGGLLERLPLTGVDVVSLDWTVDMADGRRRLGPNVAIQGNVDPGVLFGSKEFITNRIN 313
Query: 300 TILKVMGNQGHIFNLGHGMLPDLPRENAKYLVQL 333
+K G HI NLGHG+ P EN + ++
Sbjct: 314 DTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEI 347
>pdb|1EKF|A Chain A, Crystallographic Structure Of Human Branched Chain Amino
Acid Aminotransferase (Mitochondrial) Complexed With
Pyridoxal-5'-Phosphate At 1.95 Angstroms (Orthorhombic
Form
pdb|1EKF|B Chain B, Crystallographic Structure Of Human Branched Chain Amino
Acid Aminotransferase (Mitochondrial) Complexed With
Pyridoxal-5'-Phosphate At 1.95 Angstroms (Orthorhombic
Form
pdb|1EKV|A Chain A, Human Branched Chain Amino Acid Aminotransferase
(Mitochondrial): Three Dimensional Structure Of Enzyme
Inactivated By Tris Bound To The Pyridoxal-5'-Phosphate
On One End And Active Site Lys202 Nz On The Other.
pdb|1EKV|B Chain B, Human Branched Chain Amino Acid Aminotransferase
(Mitochondrial): Three Dimensional Structure Of Enzyme
Inactivated By Tris Bound To The Pyridoxal-5'-Phosphate
On One End And Active Site Lys202 Nz On The Other.
pdb|1EKP|A Chain A, Crystal Structure Of Human Branched Chain Amino Acid
Aminotransferase (Mitochondrial) Complexed With
Pyridoxal- 5'-Phosphate At 2.5 Angstroms (Monoclinic
Form).
pdb|1EKP|B Chain B, Crystal Structure Of Human Branched Chain Amino Acid
Aminotransferase (Mitochondrial) Complexed With
Pyridoxal- 5'-Phosphate At 2.5 Angstroms (Monoclinic
Form)
Length = 365
Score = 30.0 bits (66), Expect = 0.39
Identities = 15/41 (36%), Positives = 21/41 (50%)
Query: 275 GKYVLQGNLEPTRLYDKNALEEGVETILKVMGNQGHIFNLG 315
G Y L GN PT L + AL+ G E +L + G + +G
Sbjct: 199 GNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVG 239
>pdb|1M5S|A Chain A, Formylmethanofuran:tetrahydromethanopterin
Fromyltransferase From Methanosarcina Barkeri
pdb|1M5S|B Chain B, Formylmethanofuran:tetrahydromethanopterin
Fromyltransferase From Methanosarcina Barkeri
pdb|1M5S|C Chain C, Formylmethanofuran:tetrahydromethanopterin
Fromyltransferase From Methanosarcina Barkeri
pdb|1M5S|D Chain D, Formylmethanofuran:tetrahydromethanopterin
Fromyltransferase From Methanosarcina Barkeri
Length = 297
Score = 29.3 bits (64), Expect = 0.67
Identities = 21/76 (27%), Positives = 36/76 (46%), Gaps = 4/76 (5%)
Query: 214 LKFSWDYLKKISKELKKRYAHIPVI----LFPKGIGAYLDSIDGEFDVFGVDWGTPLTAA 269
LKF D ++ ++ ++ +P++ L + IGA G F +FG T LTAA
Sbjct: 121 LKFFADGMESETQIAGRKVYKVPIMEGDFLAEENIGAIAGIAGGNFFIFGDSQMTALTAA 180
Query: 270 KKILGGKYVLQGNLEP 285
+ + L+G + P
Sbjct: 181 EAAVDTIAELEGTITP 196
>pdb|1BM8| Dna-Binding Domain Of Mbp1
Length = 99
Score = 27.7 bits (60), Expect = 2.0
Identities = 19/62 (30%), Positives = 32/62 (50%), Gaps = 10/62 (16%)
Query: 118 VYDTISQTRQKLSREKALIGFCGSPWTLATYMIEGEGSKSYAKSKKMLYSEPEVLKALLE 177
VY+ I T + R+K W AT++++ + ++AK+K+ E EVLK E
Sbjct: 12 VYEFIHSTGSIMKRKK-------DDWVNATHILK---AANFAKAKRTRILEKEVLKETHE 61
Query: 178 KL 179
K+
Sbjct: 62 KV 63
>pdb|1MB1| Mbp1 From Saccharomyces Cerevisiae
Length = 130
Score = 27.7 bits (60), Expect = 2.0
Identities = 19/62 (30%), Positives = 32/62 (50%), Gaps = 10/62 (16%)
Query: 118 VYDTISQTRQKLSREKALIGFCGSPWTLATYMIEGEGSKSYAKSKKMLYSEPEVLKALLE 177
VY+ I T + R+K W AT++++ + ++AK+K+ E EVLK E
Sbjct: 15 VYEFIHSTGSIMKRKK-------DDWVNATHILK---AANFAKAKRTRILEKEVLKETHE 64
Query: 178 KL 179
K+
Sbjct: 65 KV 66
>pdb|4THI|A Chain A, Thiaminase I From Bacillus Thiaminolyticus With Covalently
Bound 4-Amino-2,5-Dimethylpyrimidine
Length = 362
Score = 25.4 bits (54), Expect = 9.7
Identities = 16/59 (27%), Positives = 26/59 (43%), Gaps = 10/59 (16%)
Query: 19 WMMRQAGRYLSEYQESRKKAGSFLELCKNSDLATEVTLQPV-EILGVDAAILFSDILVV 76
W + +GR Y ES + G D A +V +P+ G D + +SD++ V
Sbjct: 219 WFAQGSGRAFIGYSESMMRMG---------DYAEQVRFKPISSSAGQDIPLFYSDVVSV 268
>pdb|1JB9|A Chain A, Crystal Structure Of The Ferredoxin:nadp+ Reductase From
Maize Root At 1.7 Angstroms
Length = 316
Score = 25.4 bits (54), Expect = 9.7
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 280 QGNLEPTRLYDKNALEEGVETILKVMGNQGHIFNLG-HGMLPDL 322
Q N ++Y ++ +EE + I K++ HI+ G GM+P +
Sbjct: 240 QKNRSGGKMYVQDKIEEYSDEIFKLLDGGAHIYFCGLKGMMPGI 283
>pdb|2THI|A Chain A, Thiaminase I From Bacillus Thiaminolyticus
pdb|2THI|B Chain B, Thiaminase I From Bacillus Thiaminolyticus
Length = 379
Score = 25.4 bits (54), Expect = 9.7
Identities = 16/59 (27%), Positives = 26/59 (43%), Gaps = 10/59 (16%)
Query: 19 WMMRQAGRYLSEYQESRKKAGSFLELCKNSDLATEVTLQPV-EILGVDAAILFSDILVV 76
W + +GR Y ES + G D A +V +P+ G D + +SD++ V
Sbjct: 227 WFAQGSGRAFIGYSESMMRMG---------DYAEQVRFKPISSSAGQDIPLFYSDVVSV 276
>pdb|3THI|A Chain A, Thiaminase I From Bacillus Thiaminolyticus
Length = 371
Score = 25.4 bits (54), Expect = 9.7
Identities = 16/59 (27%), Positives = 26/59 (43%), Gaps = 10/59 (16%)
Query: 19 WMMRQAGRYLSEYQESRKKAGSFLELCKNSDLATEVTLQPV-EILGVDAAILFSDILVV 76
W + +GR Y ES + G D A +V +P+ G D + +SD++ V
Sbjct: 219 WFAQGSGRAFIGYSESMMRMG---------DYAEQVRFKPISSSAGQDIPLFYSDVVSV 268
>pdb|1KTB|A Chain A, The Structure Of Alpha-N-Acetylgalactosaminidase
pdb|1KTC|A Chain A, The Structure Of Alpha-N-Acetylgalactosaminidase
Length = 405
Score = 25.4 bits (54), Expect = 9.7
Identities = 14/49 (28%), Positives = 26/49 (52%), Gaps = 2/49 (4%)
Query: 257 VFGVDWGTPLTAAKKILGGKYVLQGNLEPTRLYDKNALEEG--VETILK 303
+ D T +AKKIL + ++Q N +P + + ++EG +E L+
Sbjct: 265 LMSTDLRTISPSAKKILQNRLMIQINQDPLGIQGRRIIKEGSHIEVFLR 313
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
0.319 0.138 0.400
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,931,175
Number of Sequences: 13198
Number of extensions: 82087
Number of successful extensions: 210
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: 184
Number of HSP's gapped (non-prelim): 14
length of query: 340
length of database: 2,899,336
effective HSP length: 89
effective length of query: 251
effective length of database: 1,724,714
effective search space: 432903214
effective search space used: 432903214
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)