Nitrilase Superfamily

Genome Biology 2:reviews0001.1-0001.9. Additional data file 1

Classification of publicly available nitrilase superfamily sequences into 13 branches. National Center for Biotechnology Information (NCBI) links are provided for 176 sequences in 13 branches, 12 of which resulted from non-redundant BLASTp searches (version 2.1.2, [17]) using the first sequence in each branch as the prototype for the branch. BLAST runs with each of these prototypes detect more sequences than shown in each branch. Poorly scoring sequences were generally found to be more closely related to another prototype based upon E-value and presence of signature sequences, and were assigned to branches such that no sequence belongs to more than one branch. Sequence definition lines are as provided by the host databases. It should be obvious that definition lines generated by automatic annotations or annotation jamborees are inconsistent with the branch designations provided here. The poorest scoring sequence in branch 1, the cyanide hydratase from Fusarium lateritium [30], has an artifactually poor E-value because the database sequence is not as published. Branch 13 contains outlier nitrilase-related sequences that cannot be readily classified as members of the other 12 branches and do not contain an additional fused domain.

BLASTP 2.1.2 [Nov-13-2000]


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.

Branch 1 - Nitrilase

Query= (346 letters)

Database: nr 594,795 sequences; 188,047,558 total letters

Score E
Sequences producing significant alignments: (bits) Value

sp|P32961|NRL1_ARATH NITRILASE 1 >gi|99738|pir||S22398 nitr...   689 0.0
pir||T49147 nitrilase 1 - Arabidopsis thaliana >gi|1389699|...   687 0.0
sp|P32962|NRL2_ARATH NITRILASE 2 >gi|322548|pir||S31969 nit...   613 e-174
emb|CAA68934.3| (Y07648) nitrilase 2 [Arabidopsis thaliana]      611 e-174
gb|AAB05220.1| (U38845) nitrilase 2 [Arabidopsis thaliana]       610 e-174
sp|P46010|NRL3_ARATH NITRILASE 3 >gi|11266291|pir||T49148 n...   587 e-167
sp|P46011|NRL4_ARATH NITRILASE 4 >gi|508737|gb|AAA19628.1| ...   439 e-122
pir||T03739 nitrilase (EC 3.5.5.1) 4B - common tobacco >gi|...   426 e-118
sp|Q42965|NRL4_TOBAC NITRILASE 4 >gi|7435979|pir||T03736 ni...   425 e-118
dbj|BAA77679.1| (AB027054) nitrilase-like protein [Oryza sa...   423 e-117
pir||T27679 probable nitrilase (EC 3.5.5.1) ZK1058.6 - Caen...   307 1e-82
ref|NP_012102.1| nitrilase; Nit1p [Saccharomyces cerevisiae...   193 2e-48
emb|CAA46923.1| (X66132) ORF-1 [Saccharomyces cerevisiae]        192 4e-48
pir||S77025 nitrilase (EC 3.5.5.1) - Synechocystis sp. (str...   172 7e-42
dbj|BAA11653.1| (D82961) cyanide degrading enzyme [Pseudomo...   166 5e-40
emb|CAC18136.1| (AL451011) conserved hypothetical protein [...   165 6e-40
sp|Q03217|NRL2_RHORH ALIPHATIC NITRILASE >gi|322251|pir||A4...   164 1e-39
pir||JC4212 nitrilase (EC 3.5.5.1) - Comamonas testosteroni...   159 4e-38
dbj|BAA90460.1| (AB028892) nitrilase [Bacillus sp. OxB-1]        154 1e-36
sp|Q02068|NRL1_RHORH ALIPHATIC NITRILASE >gi|322250|pir||A4...   150 3e-35
sp|P10045|NRLB_KLEPO NITRILASE, BROMOXYNIL-SPECIFIC >gi|789...   140 3e-32
sp|P32964|CYHY_GLOSO CYANIDE HYDRATASE (FORMAMIDE HYDROLYAS...   128 1e-28
sp|P20960|NRLA_ALCFA NITRILASE, ARYLACETONE-SPECIFIC (ARYLA...   125 6e-28
gb|AAF66098.1|AF192405_1 (AF192405) putative cyanide hydrat...   118 9e-26
sp|P32963|CYHY_GIBBA CYANIDE HYDRATASE (FORMAMIDE HYDROLYAS...    69 8e-11

Branch 2 - Aliphatic Amidase

Query= (346 letters)

Database: nr 594,795 sequences; 188,047,558 total letters

Score E
Sequences producing significant alignments: (bits) Value

sp|P11436|ALAM_PSEAE ALIPHATIC AMIDASE >gi|77606|pir||A2674...   684 0.0
gb|AAA25697.1| (M27612) alphatic amidase (EC 3.5.1.4) [Pseu...   681 0.0
pir||H83222 aliphatic amidase PA3366 [imported] - Pseudomon...   681 0.0
gb|AAF14257.1| (AF136599) aliphatic amidase [Bacillus stear...   581 e-165
gb|AAF69000.1|AF257487_1 (AF257487) amidase [Bacillus sp. B...   579 e-164
sp|Q01360|ALAM_RHOER ALIPHATIC AMIDASE (WIDE SPECTRUM AMIDA...   565 e-160
pir||F64556 aliphatic amidase - Helicobacter pylori (strain...   527 e-149
emb|CAA72932.1| (Y12252) AmiE protein, aliphatic amidase [H...   524 e-148
pir||B71951 aliphatic amidase - Helicobacter pylori (strain...   524 e-148
pir||F64674 aliphatic amidase - Helicobacter pylori (strain...   189 3e-47
pir||C71842 aliphatic amidase - Helicobacter pylori (strain...   184 1e-45

Branch 3 - N-terminal Amidase

Query= (457 letters)

Database: nr 594,795 sequences; 188,047,558 total letters

Score E
Sequences producing significant alignments: (bits) Value

ref|NP_012596.1| 52-kDa amidase specific for N-terminal asp... 850 0.0
pir||T39937 deamidase - fission yeast (Schizosaccharomyces ... 116 6e-25

Branch 4 - Biotinidase

Query= (523 letters)

Database: nr 594,795 sequences; 188,047,558 total letters

Score E
Sequences producing significant alignments: (bits) Value

sp|P43251|BTD_HUMAN BIOTINIDASE PRECURSOR                       1093 0.0
ref|NP_000051.1| biotinidase precursor [Homo sapiens] >gi|1... 1093 0.0
ref|NP_004657.1| vanin 1; Vannin 1 [Homo sapiens] >gi|41280...   386 e-106
gb|AAF21453.1|U39664_1 (U39664) Tiff66 [Homo sapiens]            385 e-106
ref|XP_004354.1| vanin 1 [Homo sapiens] >gi|4572585|emb|CAB...   385 e-106
ref|NP_035834.1| vanin 1; pantetheinase [Mus musculus] >gi|...   382 e-105
gb|AAF21452.1|U39663_1 (U39663) TIFF66 [Canis familiaris]        378 e-104
ref|NP_036109.1| vanin 3 [Mus musculus] >gi|6102996|emb|CAB...   373 e-102
ref|NP_060869.1| VNN3 protein [Homo sapiens] >gi|7160973|em...   370 e-101
ref|XP_004352.1| vanin 2 [Homo sapiens] >gi|4572586|emb|CAB...   359 5e-98
dbj|BAA82525.1| (D89974) glycosylphosphatidyl inositol-anch...   358 8e-98
ref|NP_004656.1| vanin 2; Vannin 2 [Homo sapiens] >gi|41280...   355 9e-97
ref|XP_004353.1| VNN3 protein [Homo sapiens]                     220 4e-56
emb|CAB77020.1| (AJ276261) vanin-like protein [Drosophila m...   162 7e-39
gb|AAG30008.1| (AF281333) biotinidase fragment 2 [Oncorhync...   151 2e-35
gb|AAF46130.1| (AE003436) CG3599 gene product [Drosophila m...   148 2e-34
gb|AAF46129.1| (AE003436) vanin-like gene product [Drosophi...   126 5e-28
gb|AAG30007.1| (AF281332) biotinidase fragment 1 [Oncorhync...    94 3e-18

Branch 5 - Beta-ureidopropionase

Query= (393 letters)

Database: nr 594,795 sequences; 188,047,558 total letters

Score E
Sequences producing significant alignments: (bits) Value

sp|Q03248|BUP_RAT BETA-UREIDOPROPIONASE (BETA-ALANINE SYNTH...   813 0.0
ref|NP_057411.1| beta-ureidopropionase [Homo sapiens] >gi|6...   684 0.0
ref|XP_009883.1| beta-ureidopropionase [Homo sapiens]            684 0.0
gb|AAF06739.1| (AF169560) beta-ureidopropionase [Homo sapiens]   679 0.0
gb|AAF54141.1| (AE003676) CG3027 gene product [Drosophila m...   502 e-141
pir||T16068 hypothetical protein F13H8.7 - Caenorhabditis e...   487 e-136
dbj|BAB09868.1| (AB008268) beta-ureidopropionase [Arabidops...   475 e-133

Branch 6 - Carbamylase

Query= (304 letters)

Database: nr 594,795 sequences; 188,047,558 total letters

Score E
Sequences producing significant alignments: (bits) Value

pir||JW0082 N-carbamyl-D-amino acid amidohydrolase (EC 3.5....   629 e-179
emb|CAA62550.1| (X91070) D-N-alpha-carbamilase [Agrobacteri...   612 e-174
gb|AAB47607.1| (U59376) N-carbamoyl-D-amino acid amidohydro...   610 e-174
pir||JW0083 N-carbamyl-D-amino acid amidohydrolase (EC 3.5....   367 e-101

Branch 7 - Prokaryotic NAD+ Synthetase

Query= (300 letters)

Database: nr 576,719 sequences; 181,542,687 total letters

Score E
Sequences producing significant alignments: (bits) Value

sp|Q9X0Y0|NAE2_THEMA PROBABLE GLUTAMINE-DEPENDENT NAD(+) SY...   607 e-173
sp|O67091|NADE_AQUAE PROBABLE GLUTAMINE-DEPENDENT NAD(+) SY...   238 8e-62
sp|P74292|NADE_SYNY3 PROBABLE GLUTAMINE-DEPENDENT NAD(+) SY...   183 2e-45
gb|AAF84763.1|AE004015_6 (AE004015) NH3-dependent NAD synth...   170 2e-41
sp|Q03638|NADE_RHOCA GLUTAMINE-DEPENDENT NAD(+) SYNTHETASE ...   158 8e-38
emb|CAB38325.1| (Y17736) NAD(+) synthase (glutamine-hydroly...   129 4e-29
sp|P71911|NADE_MYCTU GLUTAMINE-DEPENDENT NAD(+) SYNTHETASE ...   103 3e-21
pir||D70680 hypothetical protein Rv2438c - Mycobacterium tu...   103 3e-21

Branch 8 - Eukaryotic NAD+ Synthetase

Query= (360 letters)

Database: nr 576,719 sequences; 181,542,687 total letters

Score E
Sequences producing significant alignments: (bits) Value

ref|NP_011941.1| Yhr074wp >gi|731675|sp|P38795|NADE_YEAST P...   751 0.0
dbj|BAB14034.1| (AK022436) unnamed protein product [Homo sa...   457 e-128
ref|NP_060631.1| hypothetical protein FLJ10631 >gi|7022784|...   457 e-128
sp|O74940|NADE_SCHPO PUTATIVE GLUTAMINE-DEPENDENT NAD(+) SY...   442 e-123
gb|AAG12939.1|AC073944_2 (AC073944) hypothetical protein; 1...   393 e-108
sp|Q9VYA0|NADE_DROME PUTATIVE GLUTAMINE-DEPENDENT NAD(+) SY...   388 e-107
pir||T19420 hypothetical protein C24F3.4 - Caenorhabditis e...   280 1e-74

Branch 9 - Apolipoprotein N-acyltransferase

Query= (511 letters)

Database: nr 594,795 sequences; 188,047,558 total letters

Score E
Sequences producing significant alignments: (bits) Value

sp|Q9ZI86|LNT_PSEAE APOLIPOPROTEIN N-ACYLTRANSFERASE (ALP N...   770 0.0
pir||A82261 apolipoprotein N-acyltransferase VC0958 [import...   241 1e-62
gb|AAD09824.1| (AF116773) apolipoprotein N-acyltransferase ...   238 9e-62
dbj|BAA35308.1| (D90705) Apolipoprotein n-acyltransferase (...   233 4e-60
sp|P23930|LNT_ECOLI APOLIPOPROTEIN N-ACYLTRANSFERASE (ALP N...   232 7e-60
sp|P44626|LNT_HAEIN APOLIPOPROTEIN N-ACYLTRANSFERASE (ALP N...   222 9e-57
pir||H81166 apolipoprotein N-acyltransferase, probable NMB0...   155 1e-36
pir||E81938 probable apolipoprotein N-acyltransferase NMA09...   153 5e-36
sp|Q9ZDG3|LNT_RICPR APOLIPOPROTEIN N-ACYLTRANSFERASE (ALP N...   137 3e-31
sp|Q52910|LNT_RHIME APOLIPOPROTEIN N-ACYLTRANSFERASE (ALP N...   120 4e-26
emb|CAB95793.1| (AL359949) putative lipoprotein N-acyltrans...    96 8e-19
sp|O67000|LNT_AQUAE APOLIPOPROTEIN N-ACYLTRANSFERASE (ALP N...    94 3e-18
sp|P74055|LNT_SYNY3 APOLIPOPROTEIN N-ACYLTRANSFERASE (ALP N...    91 2e-17
sp|O83279|LNT_TREPA APOLIPOPROTEIN N-ACYLTRANSFERASE (ALP N...    85 2e-15
pir||G71327 probable apolipoprotein N-acyltransferase (cutE...    81 3e-14
pir||E70129 acid-inducible protein (act206) homolog - Lyme ...    81 3e-14
pir||B75407 acid tolerance protein Act206-related protein -...    80 7e-14
pir||H72359 hypothetical protein TM0573 - Thermotoga mariti...    76 1e-12
emb|CAB11299.1| (Z98604) hypothetical protein MLCB2052.01 [...    67 4e-10
pir||B70945 hypothetical protein Rv2051c - Mycobacterium tu...    67 5e-10
emb|CAC15462.1| (AJ294477) putative polyprenol-phosphate-ma...    66 8e-10
emb|CAC14382.1| (AL445963) putative transferase [Streptomyc...    66 8e-10
sp|O84539|LNT_CHLTR APOLIPOPROTEIN N-ACYLTRANSFERASE (ALP N...    56 9e-07
pir||B81662 apolipoprotein N-acetyltransferase, probable TC...    54 4e-06
pir||D71965 apolipoprotein n-acyltransferase - Helicobacter...    50 6e-05
sp|Q9Z7Q1|LNT_CHLPN APOLIPOPROTEIN N-ACYLTRANSFERASE (ALP N...    49 1e-04
pir||D64542 apolipoprotein N-acyltransferase - Helicobacter...    49 1e-04
pir||B81313 probable integral membrane protein Cj1095 [impo...    47 4e-04

Branch 10 - Nit and NitFhit

Query= (327 letters)

Database: nr 594,795 sequences; 188,047,558 total letters

Score E
Sequences producing significant alignments: (bits) Value

ref|NP_005591.1| nitrilase 1 [Homo sapiens] >gi|3228666|gb|...   677 0.0
gb|AAC40184.1| (AF069985) nitrilase homolog 1 [Mus musculus]     575 e-163
ref|NP_036179.1| nitrilase 1 [Mus musculus] >gi|3228668|gb|...   574 e-163
gb|AAF87104.1|AF284575_1 (AF284575) Nit protein 1 [Xenopus ...   372 e-102
gb|AAC39137.1| (AF069989) nitrilase and fragile histidine t...   275 4e-73
pir||T43198 nitrilase/Fhit protein - Caenorhabditis elegans...   274 1e-72
emb|CAB78004.1| (AL161512) nitrilase 1 like protein [Arabid...   248 5e-65
pir||T40601 putitive nitrilase homolog - fission yeast (Sc...   219 3e-56
pir||B69109 N-carbamoyl-D-amino acid amidohydrolase - Metha...   207 1e-52
ref|NP_012409.1| nitrilase superfamily member; Nit2p [Sacch...   196 2e-49
pir||E83086 conserved hypothetical protein PA4475 [imported...   193 2e-48
sp|P55175|Y601_SYNY3 HYPOTHETICAL 30.2 KD PROTEIN SLL0601 >...   188 9e-47
ref|NP_064587.1| Nit protein 2 [Homo sapiens] >gi|11433227|...   185 6e-46
dbj|BAA32602.1| (AB017194) hypothetical protein [Plectonema...   184 2e-45
gb|AAF87102.1|AF284573_1 (AF284573) Nit protein 2 [Mus musc...   182 4e-45
sp|Q10166|YAUB_SCHPO HYPOTHETICAL 35.7 KD PROTEIN C26A3.11 ...   169 4e-41
pir||F82325 conserved hypothetical protein VC0421 [imported...   168 9e-41
ref|NP_013455.1| nitrilase superfamily member; Nit3p [Sacch...   160 2e-38
pir||B81199 nitrilase NMB0441 [imported] - Neisseria mening...   154 2e-36
pir||E81834 conserved hypothetical protein NMA2044 [importe...   153 3e-36
pir||T48563 hypothetical protein F14F18.210 - Arabidopsis t...   153 3e-36
gb|AAF54370.1| (AE003682) CG8132 gene product [Drosophila m...   146 4e-34
pir||T36488 probable hydrolase - Streptomyces coelicolor >g...   127 1e-28
sp|P77192|YBEM_ECOLI HYPOTHETICAL 20.5 KDA PROTEIN IN CRCB-...   119 7e-26

Branch 11 - NB11

Query= (292 letters)

Database: nr 584,562 sequences; 183,936,037 total letters
Score E
Sequences producing significant alignments: (bits) Value

pir||F71901 hypothetical protein jhp0694 - Helicobacter pyl...   598 e-170
pir||E64614 beta-alanine synthetase homolog - Helicobacter ...   592 e-168
emb|CAB73204.1| (AL139076) putative hydrolase [Campylobacte...   355 3e-97
gb|AAF85242.1|AE004053_5 (AE004053) beta-alanine synthetase...   321 5e-87
emb|CAB45873.1| (Y19104) beta-alanine synthase [Lycopersico...   219 4e-56
gb|AAG03682.1|AE004467_4 (AE004467) probable hydratase [Pse...   211 7e-54
gb|AAD15597.1| (AC006232) putative nitrilase [Arabidopsis t...   201 1e-50
pir||F75263 probable hydrolase - Deinococcus radiodurans (s...   187 1e-46
ref|NP_048426.1| contains ATP/GTP-binding site motif A; sim...   174 1e-42
gb|AAD19716.1| (AF124349) hydrolase [Zymomonas mobilis]          174 1e-42
pir||T34905 probable hydrolase - Streptomyces coelicolor >g...   166 2e-40
pir||T28684 hypothetical protein - Streptomyces coelicolor ...   164 1e-39
pir||T41662 probable nitrilase - fission yeast (Schizosacch...   128 9e-29

Branch 12 - NB12

Query= (428 letters)

Database: nr 594,795 sequences; 188,047,558 total letters
Score E
Sequences producing significant alignments: (bits) Value

pir||JC4601 hypothetical 48.2k protein - Sphingomonas yanoi...   868 0.0
dbj|BAB04808.1| (AP001510) unknown conserved protein [Bacil...   322 4e-87
sp|P54608|YHCX_BACSU HYPOTHETICAL 60.2 KD PROTEIN IN CSPB-G...   322 7e-87

Non-fused Outliers

emb|CAC12333.1|  (AL445066) nitrilase related protein [Therm...
ref|NP_068956.1|  conserved hypothetical protein [Archaeoglo...
pir||G83608  probable hydratase PA0293 [imported] - Pseudomo...
pir||A72454  probable nitrilase APE2277 - Aeropyrum pernix (...
dbj|BAB04766.1|  (AP001510) unknown conserved protein [Bacil...
pir||H82556  beta-alanine synthetase XF2443 [imported] - Xyl...
pir||E69863  conserved hypothetical protein ykrU - Bacillus ...
pir||B83387  hypothetical protein PA2074 [imported] - Pseudo...
sp|Q11146|Y480_MYCTU  HYPOTHETICAL 35.2 KDA PROTEIN RV0480C ...
gb|AAD19716.1|  (AF124349) hydrolase [Zymomonas mobilis]       
sp|P55176|YPQQ_PSEFL  HYPOTHETICAL 31.2 KD PROTEIN IN PQQF 5...
pir||E64614  beta-alanine synthetase homolog - Helicobacter ...
pir||F71901  hypothetical protein jhp0694 - Helicobacter pyl...
gb|AAD15597.1|  (AC006232) putative nitrilase [Arabidopsis t...
sp|P55178|YAG5_STALU  HYPOTHETICAL PROTEIN IN AGR OPERON (OR...
gb|AAC38297.1|  (AF012132) unknown [Staphylococcus epidermidis]
sp|P55177|YAG5_STAAU  HYPOTHETICAL 29.8 KD PROTEIN IN AGR OP...
emb|CAB76877.1|  (AL159139) putative hydrolase [Streptomyces...
pir||G71949  hypothetical protein jhp0294 - Helicobacter pyl...
pir||E64558  conserved hypothetical protein HP0309 - Helicob...
pir||A70310  conserved hypothetical protein aq_103 - Aquifex...
pir||C71109  hypothetical protein PH0642 - Pyrococcus horiko...
pir||H83195  conserved hypothetical protein PA3598 [imported...
pir||B81369  probable hydrolase Cj0947c [imported] - Campylo...
gb|AAG19366.1|  (AE005031) Vng0936c [Halobacterium sp. NRC-1]  
pir||C75051  hydrolase related PAB1449 - Pyrococcus abyssi (...