Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate RR42_RS09905 RR42_RS09905 fumarylacetoacetase
Query= SwissProt::P25093 (419 letters) >lcl|FitnessBrowser__Cup4G11:RR42_RS09905 RR42_RS09905 fumarylacetoacetase Length = 437 Score = 338 bits (868), Expect = 1e-97 Identities = 191/427 (44%), Positives = 254/427 (59%), Gaps = 25/427 (5%) Query: 7 AEDSDFPIQNLPYGVFSTQSNPKP-RIGVAIGDQILDLSVIKHLFTGPVL----SKHQHV 61 A DFP+QNLP VF + + + R GVAIGDQI+DL ++ L P L ++ Sbjct: 20 AAGCDFPLQNLPLSVFRRKGSTEAWRGGVAIGDQIVDLGALQSL---PGLQDSAAEAVRA 76 Query: 62 FDETTLNSFMGLGQAAWKEARASLQNLLSASQAQLRDDKELRQRAFTSQASATMHLPATI 121 TLN + LG +W+ R L LL + + R +E A Q A +P I Sbjct: 77 AAAPTLNGLLELGPESWRALRHGLYGLLQSGSSLARQVRE----ALVPQLDAEHAVPVRI 132 Query: 122 GDYTDFYSSLQHATNVGIMFRGKENALLPNWLHLPVGYHGRASSVVVSGTPIRRPMGQMR 181 GDYTDFY+SL HA N F + N PN+ LP+ YHGR SS+ VSG + RP GQ R Sbjct: 133 GDYTDFYTSLDHAVNCCRQFGIEVN---PNFDWLPIAYHGRVSSIDVSGQQVYRPAGQYR 189 Query: 182 PDNSKPPVYGASKRLDMELEMAFFVGPGNRFGEPIPISKAQEHIFGMVLMNDWSARDIQQ 241 D S PVYG +RLD ELE+ +G GN G PIP++ AQ+HIFG+ L+NDWSARDIQ Sbjct: 190 TDPSSAPVYGPCQRLDYELEVGAVIGIGNARGTPIPLANAQQHIFGLCLLNDWSARDIQT 249 Query: 242 WEYVPLGPFLGKSFGTTISPWVVPMDALMPFVV--PNPKQDPKPLPYL---CHSQPYTFD 296 WE PLGPFL K+F TT+SPW+V ++AL+P+ + P+PL YL ++ FD Sbjct: 250 WEMQPLGPFLAKNFATTLSPWIVTLEALLPYRTGWTRAPERPQPLDYLRSADNAAAGAFD 309 Query: 297 INLSVA-LKGEGMSQAA---TICRSNFKHMYWTILQQLTHHSVNGCNLRPGDLLASGTIS 352 I L V+ L +Q + R++F+H YWT+ Q + HH+V GCNL+PGDLL SGT+S Sbjct: 310 IQLEVSILSARRQAQGRPPHKLTRTSFQHQYWTLGQMIAHHTVGGCNLQPGDLLGSGTVS 369 Query: 353 GSDPESFGSMLELSWKGTKAIDVGQGQTRTFLLDGDEVIITGHCQGDGY-RVGFGQCAGK 411 G +P G+++EL+ GT D+G G+ R FL DGD V+ G C+ + Y R+GFG Sbjct: 370 GPNPWEAGALIELTVSGTHPADIGDGEQRGFLKDGDTVVFRGWCEREDYARIGFGVNYAT 429 Query: 412 VLPALSP 418 VLPA P Sbjct: 430 VLPAPGP 436 Lambda K H 0.320 0.136 0.422 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: 582 Number of extensions: 29 Number of successful extensions: 7 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: 437 Length adjustment: 32 Effective length of query: 387 Effective length of database: 405 Effective search space: 156735 Effective search space used: 156735 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 RR42_RS09905 RR42_RS09905 (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.25801.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-143 464.5 0.0 1.8e-143 464.3 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS09905 RR42_RS09905 fumarylacetoacetase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS09905 RR42_RS09905 fumarylacetoacetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 464.3 0.0 1.8e-143 1.8e-143 1 419 [. 13 433 .. 13 434 .. 0.93 Alignments for each domain: == domain 1 score: 464.3 bits; conditional E-value: 1.8e-143 TIGR01266 1 sfvavak..nsdfplqnlPyGvfstkads.srrigvaiGdqildlskiaaaglfeglalkehqevfkes 66 s++++a+ +dfplqnlP+ vf k ++ r gvaiGdqi+dl ++++ ++++ ++ e+ + lcl|FitnessBrowser__Cup4G11:RR42_RS09905 13 SWLDSANaaGCDFPLQNLPLSVFRRKGSTeAWRGGVAIGDQIVDLGALQSLPGLQD-SAAEAVRAAAAP 80 79988885467************976544156899***************888887.567788889999 PP TIGR01266 67 tlnaflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirha 135 tln +l lg +++++r+ l ll + + a++ +eal++q +a+ +P++iGdytdfy+s+ ha lcl|FitnessBrowser__Cup4G11:RR42_RS09905 81 TLNGLLELGPESWRALRHGLYGLLQSGSSL----ARQVREALVPQLDAEHAVPVRIGDYTDFYTSLDHA 145 ************************976666....777889***************************** PP TIGR01266 136 tnvGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelela 204 n f + Pn+ +lP++yhGr ss+ vsG ++ rP Gq ++d ++ Pv+gpc++ld+ele++ lcl|FitnessBrowser__Cup4G11:RR42_RS09905 146 VNCCRQFG---IEVNPNFDWLPIAYHGRVSSIDVSGQQVYRPAGQYRTDPSSAPVYGPCQRLDYELEVG 211 ****9998...5678****************************************************** PP TIGR01266 205 ffvgtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePf 273 +g +n+ G+++p+ +a++hifG++llndwsardiq+we +PlGPflak+fatt+sPw+v++eal P+ lcl|FitnessBrowser__Cup4G11:RR42_RS09905 212 AVIGIGNARGTPIPLANAQQHIFGLCLLNDWSARDIQTWEMQPLGPFLAKNFATTLSPWIVTLEALLPY 280 ********************************************************************* PP TIGR01266 274 rvaqlePeqdpkplpylredr..adtafdielevslkteGlae....aavisrsnakslywtlkqqlah 336 r+ ++ ++p+pl ylr + a afdi+levs+ ++ + +++++r+ +++ ywtl q++ah lcl|FitnessBrowser__Cup4G11:RR42_RS09905 281 RTGWTRAPERPQPLDYLRSADnaAAGAFDIQLEVSILSARRQAqgrpPHKLTRTSFQHQYWTLGQMIAH 349 ***99*9**********975435889**********987654456779********************* PP TIGR01266 337 hsvnGcnlraGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckkeGv 405 h+v Gcnl++GdllgsGt+sG+++ + G+l+el+ G+++ +++dge+r fl+dGd+v++rg c++e + lcl|FitnessBrowser__Cup4G11:RR42_RS09905 350 HTVGGCNLQPGDLLGSGTVSGPNPWEAGALIELTVSGTHPADIGDGEQRGFLKDGDTVVFRGWCEREDY 418 ******************************************************************998 PP TIGR01266 406 r.vGfGecaGkvlpa 419 +GfG +vlpa lcl|FitnessBrowser__Cup4G11:RR42_RS09905 419 ArIGFGVNYATVLPA 433 77***********97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (437 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.22 // [ok]
This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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