Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate BPHYT_RS03805 BPHYT_RS03805 fumarylacetoacetase
Query= BRENDA::P35505 (419 letters) >FitnessBrowser__BFirm:BPHYT_RS03805 Length = 436 Score = 499 bits (1285), Expect = e-146 Identities = 241/419 (57%), Positives = 302/419 (72%), Gaps = 4/419 (0%) Query: 2 SFIPVAEDS--DFPIQNLPYGVFSTQSNPKPRIGVAIGDQILDLSVIKH--LFTGPALSK 57 S++ A DS DF IQNLP+GVFS N R+GVAIGD I+DL+ ++ L + P+ + Sbjct: 17 SWVESANDSTNDFSIQNLPFGVFSDHLNATRRVGVAIGDGIVDLAALESAGLLSVPSSAA 76 Query: 58 HQHVFDETTLNNFMGLGQAAWKEARASLQNLLSASQARLRDDKELRQRAFTSQASATMHL 117 VF LN+F+ LG+ AW+ R L LLS A LRDD ELR RA QA A +HL Sbjct: 77 GNSVFVRDALNDFIALGRDAWRGVRIQLSKLLSRDNATLRDDAELRGRALIRQADAQLHL 136 Query: 118 PATIGDYTDFYSSRQHATNVGIMFRGKENALLPNWLHLPVGYHGRASSIVVSGTPIRRPM 177 P I YTDFYSS++HATNVG MFR +NALLPNW +P+GY+GRASS+VVSGTP+RRP Sbjct: 137 PVQIPGYTDFYSSKEHATNVGSMFRDPKNALLPNWSEMPIGYNGRASSVVVSGTPVRRPN 196 Query: 178 GQMRPDNSKPPVYGACRLLDMELEMAFFVGPGNRFGEPIPISKAHEHIFGMVLMNDWSAR 237 GQ++ + PV+GACR LD+ELE F +G GN GEP+ + A HIFGMVL+NDWSAR Sbjct: 197 GQLKLPDQDRPVFGACRKLDIELETGFVIGAGNALGEPVACADAEAHIFGMVLLNDWSAR 256 Query: 238 DIQQWEYVPLGPFLGKSFGTTISPWVVPMDALMPFVVPNPKQDPKPLPYLCHSQPYTFDI 297 DIQQWEYVPLGPF K F TTISPW+V +DAL PF V P Q+ +PL YL H + FDI Sbjct: 257 DIQQWEYVPLGPFNSKGFATTISPWIVTLDALEPFRVAQPAQELQPLAYLRHEGEHAFDI 316 Query: 298 NLSVSLKGEGMSQAATICRSNFKHMYWTMLQQLTHHSVNGCNLRPGDLLASGTISGSDPE 357 L V L+ + +A+TI R+NFKHMYWTM QQL HH+V+GCN R GDL+ SGTISG + Sbjct: 317 TLEVRLRPQQAKEASTISRTNFKHMYWTMAQQLAHHTVSGCNTRVGDLMGSGTISGPTED 376 Query: 358 SFGSMLELSWKGTKAIDVEQGQTRTFLLDGDEVIITGHCQGDGYRVGFGQCAGKVLPAL 416 SFGS+LE++W G K +++++G TR+F+ DGDE+ + G CQGDGYRVGFG C G++LPAL Sbjct: 377 SFGSLLEMTWNGKKPLNLQEGGTRSFIEDGDELTLAGWCQGDGYRVGFGACVGEILPAL 435 Lambda K H 0.320 0.136 0.426 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: 605 Number of extensions: 21 Number of successful extensions: 2 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: 436 Length adjustment: 32 Effective length of query: 387 Effective length of database: 404 Effective search space: 156348 Effective search space used: 156348 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 BPHYT_RS03805 BPHYT_RS03805 (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.1872162.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-189 616.4 0.0 1.3e-189 616.3 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS03805 BPHYT_RS03805 fumarylacetoacetas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS03805 BPHYT_RS03805 fumarylacetoacetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 616.3 0.0 1.3e-189 1.3e-189 1 420 [] 17 435 .. 17 435 .. 0.99 Alignments for each domain: == domain 1 score: 616.3 bits; conditional E-value: 1.3e-189 TIGR01266 1 sfvavakns..dfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevfkestl 68 s+v++a++s df++qnlP+Gvfs + +++rr+gvaiGd i+dl+++ +agl++ ++ + + vf + +l lcl|FitnessBrowser__BFirm:BPHYT_RS03805 17 SWVESANDStnDFSIQNLPFGVFSDHLNATRRVGVAIGDGIVDLAALESAGLLSVPSSAAGNSVFVRDAL 86 8*****965559********************************************************** PP TIGR01266 69 naflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhatnv 138 n f+algr a++ vr +l klls ++++lrd+a+lr +al+ qa+a+ hlP+qi ytdfyss +hatnv lcl|FitnessBrowser__BFirm:BPHYT_RS03805 87 NDFIALGRDAWRGVRIQLSKLLSRDNATLRDDAELRGRALIRQADAQLHLPVQIPGYTDFYSSKEHATNV 156 ********************************************************************** PP TIGR01266 139 GilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaffvg 208 G +fr ++nallPn+ +P+gy GrassvvvsGt++rrP+Gq+k ++ + Pvfg+c+kld+ele +f +g lcl|FitnessBrowser__BFirm:BPHYT_RS03805 157 GSMFRDPKNALLPNWSEMPIGYNGRASSVVVSGTPVRRPNGQLKLPDQDRPVFGACRKLDIELETGFVIG 226 ********************************************************************** PP TIGR01266 209 tenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfrvaql 278 +n+lGe+v ae hifG+vllndwsardiq+weyvPlGPf++k fatt+sPw+v+++alePfrva lcl|FitnessBrowser__BFirm:BPHYT_RS03805 227 AGNALGEPVACADAEAHIFGMVLLNDWSARDIQQWEYVPLGPFNSKGFATTISPWIVTLDALEPFRVA-- 294 *******************************************************************9.. PP TIGR01266 279 ePeqdpkplpylredradtafdielevslkteGlaeaavisrsnakslywtlkqqlahhsvnGcnlraGd 348 +P q+ +pl+ylr++ + afdi lev l+++ +ea++isr+n+k++ywt++qqlahh+v+Gcn r Gd lcl|FitnessBrowser__BFirm:BPHYT_RS03805 295 QPAQELQPLAYLRHE-GEHAFDITLEVRLRPQQAKEASTISRTNFKHMYWTMAQQLAHHTVSGCNTRVGD 363 9**************.999*************************************************** PP TIGR01266 349 llgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckkeGvrvGfGecaGkvlp 418 l+gsGtisG+ e++fGslle++++Gkk+++l +g tr f+edGde+ l g c+ +G+rvGfG c G++lp lcl|FitnessBrowser__BFirm:BPHYT_RS03805 364 LMGSGTISGPTEDSFGSLLEMTWNGKKPLNLQEGGTRSFIEDGDELTLAGWCQGDGYRVGFGACVGEILP 433 ********************************************************************** PP TIGR01266 419 al 420 al lcl|FitnessBrowser__BFirm:BPHYT_RS03805 434 AL 435 95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (436 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 23.72 // [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:
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