Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate WP_029000797.1 H537_RS0129855 fumarylacetoacetase
Query= SwissProt::P16930 (419 letters) >NCBI__GCF_000430725.1:WP_029000797.1 Length = 438 Score = 399 bits (1025), Expect = e-116 Identities = 209/419 (49%), Positives = 275/419 (65%), Gaps = 17/419 (4%) Query: 9 DSDFPIHNLPYGVFSTRGDPRP-RIGVAIGDQILDLSIIKHLFT-GPVLSKHQDVFNQPT 66 D+ FPI NLP+ VF +G R GVAIGDQI+DL+ + G + +Q Sbjct: 23 DTGFPIQNLPFAVFRRKGSAEAFRGGVAIGDQIVDLAAVAASGEIGGAAGEAVRAASQDK 82 Query: 67 LNSFMGLGQAAWKEARVFLQNLLSVSQARLRDDTELRKCAFISQASATMHLPATIGDYTD 126 LN+ M LG+ AW R+ L L A + LR C + QA A +PA IGDYTD Sbjct: 83 LNALMALGRPAWAALRLALSRALRQGAA---EQEPLRTC-LVPQAEAEYDVPARIGDYTD 138 Query: 127 FYSSRQHATNVGIMFRDKENALMPNWLHLPVGYHGRASSVVVSGTPIRRPMGQMKPDDSK 186 FY+S HATN+G +FR +N L+PN+ +P+GYHGRASS+ VSG RRP+GQ P + Sbjct: 139 FYTSVHHATNIGRLFRP-DNPLLPNYKWVPIGYHGRASSIGVSGQAFRRPVGQTLPVGAA 197 Query: 187 PPVYGACKLLDMELEMAFFVGPGNRLGEPIPISKAHEHIFGMVLMNDWSARDIQKWEYVP 246 PV G + LD+ELE+ F+G GN LGEP+ I++A +H+FG+ L+NDWSARDIQ WEY P Sbjct: 198 QPVAGPSRALDIELELGVFIGSGNTLGEPVAITEAEDHVFGICLLNDWSARDIQAWEYQP 257 Query: 247 LGPFLGKSFGTTVSPWVVPMDALMPFAVP--NPKQDPRPLPYL-CHDEPYT--FDINLSV 301 LGPFL KSF TT+SPW+V ++AL PF VP P+ DP+PLPYL C +T FDI L V Sbjct: 258 LGPFLSKSFATTISPWIVTLEALAPFRVPFVRPEGDPQPLPYLDCEANRHTGAFDIQLQV 317 Query: 302 NL----KGEGMSQAATICKSNFKYMYWTMLQQLTHHSVNGCNLRPGDLLASGTISGPEPE 357 L E S AATIC++++++ YWT+ Q + HH+V GCNL+PGDL SGT+SGP P+ Sbjct: 318 ELLTPRLREAGSAAATICRTSYRHAYWTVAQMVAHHTVGGCNLQPGDLFGSGTLSGPTPD 377 Query: 358 NFGSMLELSWKGTKPIDLGNGQTRKFLLDGDEVIITGYCQGDG-YRIGFGQCAGKVLPA 415 G+++EL+ G +P+ L G+ R FL DGD V+I G+C+ G RIGFG+C G VLPA Sbjct: 378 QAGALIELTAGGKQPLQLPGGEQRTFLEDGDSVVIRGWCEKPGAVRIGFGECVGTVLPA 436 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: 589 Number of extensions: 32 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: 438 Length adjustment: 32 Effective length of query: 387 Effective length of database: 406 Effective search space: 157122 Effective search space used: 157122 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_029000797.1 H537_RS0129855 (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.7826.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-174 565.0 0.0 5.5e-174 564.8 0.0 1.0 1 lcl|NCBI__GCF_000430725.1:WP_029000797.1 H537_RS0129855 fumarylacetoaceta Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000430725.1:WP_029000797.1 H537_RS0129855 fumarylacetoacetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 564.8 0.0 5.5e-174 5.5e-174 1 419 [. 14 436 .. 14 437 .. 0.94 Alignments for each domain: == domain 1 score: 564.8 bits; conditional E-value: 5.5e-174 TIGR01266 1 sfvavak..nsdfplqnlPyGvfstkads.srrigvaiGdqildlskiaaaglfeglalkehqevfkes 66 s+va+a+ ++ fp+qnlP+ vf k ++ r gvaiGdqi+dl+++aa+g g a++e+ + ++ lcl|NCBI__GCF_000430725.1:WP_029000797.1 14 SWVASANtaDTGFPIQNLPFAVFRRKGSAeAFRGGVAIGDQIVDLAAVAASGEIGG-AAGEAVRAASQD 81 8****9955556***********976554145889*******************99.999********* PP TIGR01266 67 tlnaflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirha 135 lna++algrpa+ ++r l + l + a+ ++ + l++qaea+ +Pa+iGdytdfy+s++ha lcl|NCBI__GCF_000430725.1:WP_029000797.1 82 KLNALMALGRPAWAALRLALSRALRQGAAE----QEPLRTCLVPQAEAEYDVPARIGDYTDFYTSVHHA 146 ******************999999844333....44455789*************************** PP TIGR01266 136 tnvGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelela 204 tn+G lfr +dn+llPnyk++P+gyhGrass+ vsG rrPvGq+++ +a +Pv gp++ ld+elel+ lcl|NCBI__GCF_000430725.1:WP_029000797.1 147 TNIGRLFR-PDNPLLPNYKWVPIGYHGRASSIGVSGQAFRRPVGQTLPVGAAQPVAGPSRALDIELELG 214 ********.************************************************************ PP TIGR01266 205 ffvgtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePf 273 +f+g++n+lGe+v i ae+h+fG++llndwsardiqawey+PlGPfl+ksfatt+sPw+v++eal Pf lcl|NCBI__GCF_000430725.1:WP_029000797.1 215 VFIGSGNTLGEPVAITEAEDHVFGICLLNDWSARDIQAWEYQPLGPFLSKSFATTISPWIVTLEALAPF 283 ********************************************************************* PP TIGR01266 274 rvaqlePeqdpkplpylr.edr.adtafdielevslkteGlae....aavisrsnakslywtlkqqlah 336 rv+ ++Pe+dp+plpyl e + + afdi+l+v+l t l+e aa+i+r+ ++ ywt++q++ah lcl|NCBI__GCF_000430725.1:WP_029000797.1 284 RVPFVRPEGDPQPLPYLDcEANrHTGAFDIQLQVELLTPRLREagsaAATICRTSYRHAYWTVAQMVAH 352 *****************6243337789********98876666565599******************** PP TIGR01266 337 hsvnGcnlraGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckkeGv 405 h+v Gcnl++Gdl+gsGt+sG+ +++ G+l+el+a+Gk++++l ge+r+fledGd v++rg c+k G lcl|NCBI__GCF_000430725.1:WP_029000797.1 353 HTVGGCNLQPGDLFGSGTLSGPTPDQAGALIELTAGGKQPLQLPGGEQRTFLEDGDSVVIRGWCEKPGA 421 ********************************************************************8 PP TIGR01266 406 r.vGfGecaGkvlpa 419 + +GfGec G+vlpa lcl|NCBI__GCF_000430725.1:WP_029000797.1 422 VrIGFGECVGTVLPA 436 77************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (438 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.08 // [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