Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate WP_029000002.1 H537_RS0124835 fumarylacetoacetase
Query= SwissProt::P16930 (419 letters) >NCBI__GCF_000430725.1:WP_029000002.1 Length = 442 Score = 399 bits (1025), Expect = e-116 Identities = 210/420 (50%), Positives = 276/420 (65%), Gaps = 19/420 (4%) Query: 10 SDFPIHNLPYGVFSTRGDPRP-RIGVAIGDQILDLSIIKHL--FTGPVLSKHQDVFNQPT 66 +DFPI NLP+ VF +G R GVAIGDQI+DL+ L F GP +Q Sbjct: 24 TDFPIQNLPFAVFRRKGSLEAWRGGVAIGDQIVDLAAAAALAVFDGPA-GMAALAGSQDK 82 Query: 67 LNSFMGLGQAAWKEARVFLQNLLSVSQARLRDDTELRKCAFISQASATMHLPATIGDYTD 126 LN+ M GQ AW+ R+ L L A R +L+ C + QA A +PA IGDYTD Sbjct: 83 LNALMARGQPAWRALRLALSRGLREGAAEQR---QLQAC-LVPQAEAEYDVPARIGDYTD 138 Query: 127 FYSSRQHATNVGIMFRDKENALMPNWLHLPVGYHGRASSVVVSGTPIRRPMGQMKPDDSK 186 FY+S HATN+G +FR +N L+PN+ +P+GYHGRASS+ VSG RRP GQ P + Sbjct: 139 FYTSVHHATNIGRLFRP-DNPLLPNYKWVPIGYHGRASSIGVSGQAFRRPQGQTLPPGAA 197 Query: 187 PPVYGACKLLDMELEMAFFVGPGNRLGEPIPISKAHEHIFGMVLMNDWSARDIQKWEYVP 246 PV G CK LD+ELE+ F+G GN LG P+ I++A +H+FG+ L+NDWSARDIQ WEY P Sbjct: 198 QPVAGPCKRLDIELELGVFIGEGNALGGPVAIAQAEDHVFGICLLNDWSARDIQAWEYQP 257 Query: 247 LGPFLGKSFGTTVSPWVVPMDALMPFAVP--NPKQDPRPLPYL---CHDEPYTFDINLSV 301 LGPFL KSF TT+SPW+V ++AL P+ P P+ DP+PLPYL H E + DI L V Sbjct: 258 LGPFLSKSFATTISPWIVTLEALAPYRAPFQRPEGDPQPLPYLDCAAHREAGSLDIQLQV 317 Query: 302 NLKGEGMSQA----ATICKSNFKYMYWTMLQQLTHHSVNGCNLRPGDLLASGTISGPEPE 357 L M +A AT+C++++++ YWT+ Q +THH+VNGCNL+PGDLL SGT+SGP + Sbjct: 318 ELLTPRMREAGHAPATLCRTSYRHAYWTLAQMVTHHTVNGCNLQPGDLLGSGTLSGPTLD 377 Query: 358 NFGSMLELSWKGTKPIDLGNGQTRKFLLDGDEVIITGYCQGDG-YRIGFGQCAGKVLPAL 416 G+++EL+ G +P+ L G+ R FL DGD V++ G+C+ G RIGFG C G VLPAL Sbjct: 378 QAGALIELTGGGKQPVALPGGEQRTFLEDGDSVVLRGWCEKPGAARIGFGLCEGTVLPAL 437 Lambda K H 0.321 0.139 0.440 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 623 Number of extensions: 37 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 419 Length of database: 442 Length adjustment: 32 Effective length of query: 387 Effective length of database: 410 Effective search space: 158670 Effective search space used: 158670 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
Align candidate WP_029000002.1 H537_RS0124835 (fumarylacetoacetase)
to HMM TIGR01266 (fahA: fumarylacetoacetase (EC 3.7.1.2))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR01266.hmm # target sequence database: /tmp/gapView.13199.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01266 [M=420] Accession: TIGR01266 Description: fum_ac_acetase: fumarylacetoacetase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-171 554.4 0.0 9.3e-171 554.2 0.0 1.0 1 lcl|NCBI__GCF_000430725.1:WP_029000002.1 H537_RS0124835 fumarylacetoaceta Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000430725.1:WP_029000002.1 H537_RS0124835 fumarylacetoacetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 554.2 0.0 9.3e-171 9.3e-171 1 420 [] 14 437 .. 14 437 .. 0.94 Alignments for each domain: == domain 1 score: 554.2 bits; conditional E-value: 9.3e-171 TIGR01266 1 sfvavak..nsdfplqnlPyGvfstkads.srrigvaiGdqildlskiaaaglfeglalkehqevfkes 66 s+va+a+ +dfp+qnlP+ vf k ++ r gvaiGdqi+dl+++aa ++f+g+a ++ + ++ lcl|NCBI__GCF_000430725.1:WP_029000002.1 14 SWVASAHraGTDFPIQNLPFAVFRRKGSLeAWRGGVAIGDQIVDLAAAAALAVFDGPAG-MAALAGSQD 81 89999985567************977655156899*********************765.556678899 PP TIGR01266 67 tlnaflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirha 135 lna++a g+pa++++r l + l e a+ +++ + l++qaea+ +Pa+iGdytdfy+s++ha lcl|NCBI__GCF_000430725.1:WP_029000002.1 82 KLNALMARGQPAWRALRLALSRGLREGAAE----QRQLQACLVPQAEAEYDVPARIGDYTDFYTSVHHA 146 9****************9999888855544....34446789*************************** PP TIGR01266 136 tnvGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelela 204 tn+G lfr +dn+llPnyk++P+gyhGrass+ vsG rrP+Gq+++++a +Pv gpck+ld+elel+ lcl|NCBI__GCF_000430725.1:WP_029000002.1 147 TNIGRLFR-PDNPLLPNYKWVPIGYHGRASSIGVSGQAFRRPQGQTLPPGAAQPVAGPCKRLDIELELG 214 ********.************************************************************ PP TIGR01266 205 ffvgtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePf 273 +f+g++n+lG +v i +ae+h+fG++llndwsardiqawey+PlGPfl+ksfatt+sPw+v++eal P+ lcl|NCBI__GCF_000430725.1:WP_029000002.1 215 VFIGEGNALGGPVAIAQAEDHVFGICLLNDWSARDIQAWEYQPLGPFLSKSFATTISPWIVTLEALAPY 283 ********************************************************************* PP TIGR01266 274 rvaqlePeqdpkplpylr..edradtafdielevslkteGlae....aavisrsnakslywtlkqqlah 336 r + +Pe+dp+plpyl +r+ ++di+l+v+l t ++e +a+++r+ ++ ywtl+q+++h lcl|NCBI__GCF_000430725.1:WP_029000002.1 284 RAPFQRPEGDPQPLPYLDcaAHREAGSLDIQLQVELLTPRMREaghaPATLCRTSYRHAYWTLAQMVTH 352 *****************6224558999*********999888877779********************* PP TIGR01266 337 hsvnGcnlraGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckkeGv 405 h+vnGcnl++GdllgsGt+sG+ ++ G+l+el+ +Gk++v l ge+r+fledGd v+lrg c+k G lcl|NCBI__GCF_000430725.1:WP_029000002.1 353 HTVNGCNLQPGDLLGSGTLSGPTLDQAGALIELTGGGKQPVALPGGEQRTFLEDGDSVVLRGWCEKPGA 421 ********************************************************************8 PP TIGR01266 406 r.vGfGecaGkvlpal 420 +GfG c G+vlpal lcl|NCBI__GCF_000430725.1:WP_029000002.1 422 ArIGFGLCEGTVLPAL 437 77************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (442 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.58 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory