Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate H281DRAFT_04742 H281DRAFT_04742 fumarylacetoacetate hydrolase
Query= SwissProt::P16930 (419 letters) >FitnessBrowser__Burk376:H281DRAFT_04742 Length = 433 Score = 504 bits (1299), Expect = e-147 Identities = 239/408 (58%), Positives = 302/408 (74%), Gaps = 5/408 (1%) Query: 10 SDFPIHNLPYGVFSTRGDPRPRIGVAIGDQILDLSIIKH--LFTGPVLSKHQDVFNQPTL 67 +DF I NLP+G+FS D PR+GVAIGD+I+DL+ ++ L T P + VF + TL Sbjct: 27 NDFSIQNLPFGIFSDSKDDTPRVGVAIGDEIVDLAALEAAGLLTVP---SNAGVFARDTL 83 Query: 68 NSFMGLGQAAWKEARVFLQNLLSVSQARLRDDTELRKCAFISQASATMHLPATIGDYTDF 127 N F+ LG+ AW+ R+ L NLLS A LRDD LR A + QA A +HLP I YTDF Sbjct: 84 NEFIALGRDAWRSVRIQLSNLLSRDTATLRDDAALRAKALVRQADARLHLPVQIPGYTDF 143 Query: 128 YSSRQHATNVGIMFRDKENALMPNWLHLPVGYHGRASSVVVSGTPIRRPMGQMKPDDSKP 187 YSS++HATNVG MFR+ ++AL+PNW +P+GY+GRASSVVVSGTP+RRP GQ+K D + Sbjct: 144 YSSKEHATNVGSMFRNPKDALLPNWSEMPIGYNGRASSVVVSGTPVRRPNGQLKLPDQER 203 Query: 188 PVYGACKLLDMELEMAFFVGPGNRLGEPIPISKAHEHIFGMVLMNDWSARDIQKWEYVPL 247 PV+GAC+ LD+ELE F +G GN LGEPI + A HIFGMVL+NDWSARDIQ+WEYVPL Sbjct: 204 PVFGACRKLDIELETGFVIGGGNALGEPIACTDAEAHIFGMVLLNDWSARDIQQWEYVPL 263 Query: 248 GPFLGKSFGTTVSPWVVPMDALMPFAVPNPKQDPRPLPYLCHDEPYTFDINLSVNLKGEG 307 GPF KSF TT+SPW+V +DAL PF V P Q+P+PL YL HD + FDI L V L+ +G Sbjct: 264 GPFNSKSFTTTISPWIVTLDALEPFRVAQPVQEPQPLAYLRHDGEHAFDIALEVTLRPQG 323 Query: 308 MSQAATICKSNFKYMYWTMLQQLTHHSVNGCNLRPGDLLASGTISGPEPENFGSMLELSW 367 QA TI ++NFKYMYWTM QQL HH+V GCN R GDL+ SGTISGP +++GS+LEL+ Sbjct: 324 AKQATTIARTNFKYMYWTMAQQLAHHTVGGCNTRVGDLMGSGTISGPTEDSYGSLLELTL 383 Query: 368 KGTKPIDLGNGQTRKFLLDGDEVIITGYCQGDGYRIGFGQCAGKVLPA 415 G KP++L G TR F+ DGDE+ ++G+CQ DGYR+GFG C G++LPA Sbjct: 384 NGKKPLELNEGGTRSFIEDGDELTLSGWCQADGYRVGFGTCVGEILPA 431 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: 593 Number of extensions: 18 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: 433 Length adjustment: 32 Effective length of query: 387 Effective length of database: 401 Effective search space: 155187 Effective search space used: 155187 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 H281DRAFT_04742 H281DRAFT_04742 (fumarylacetoacetate hydrolase)
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.12549.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-190 617.6 0.0 5.9e-190 617.4 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_04742 H281DRAFT_04742 fumarylacetoacet Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_04742 H281DRAFT_04742 fumarylacetoacetate hydrolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 617.4 0.0 5.9e-190 5.9e-190 1 419 [. 17 431 .. 17 432 .. 0.99 Alignments for each domain: == domain 1 score: 617.4 bits; conditional E-value: 5.9e-190 TIGR01266 1 sfvavak..nsdfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevfk 64 s+v++a+ df++qnlP+G+fs ++d ++r+gvaiGd+i+dl+++ aagl++ +++ vf lcl|FitnessBrowser__Burk376:H281DRAFT_04742 17 SWVQSANepSNDFSIQNLPFGIFSDSKDDTPRVGVAIGDEIVDLAALEAAGLLTV---PSNAGVFA 79 8*****96668****************************************9987...67899*** PP TIGR01266 65 estlnaflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfys 130 + tln f+algr a++ vr +l +lls ++++lrd+aalr +al+ qa+a+ hlP+qi ytdfys lcl|FitnessBrowser__Burk376:H281DRAFT_04742 80 RDTLNEFIALGRDAWRSVRIQLSNLLSRDTATLRDDAALRAKALVRQADARLHLPVQIPGYTDFYS 145 ****************************************************************** PP TIGR01266 131 sirhatnvGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckk 196 s +hatnvG +fr +++allPn+ +P+gy GrassvvvsGt++rrP+Gq+k ++ + Pvfg+c+k lcl|FitnessBrowser__Burk376:H281DRAFT_04742 146 SKEHATNVGSMFRNPKDALLPNWSEMPIGYNGRASSVVVSGTPVRRPNGQLKLPDQERPVFGACRK 211 ****************************************************************** PP TIGR01266 197 ldlelelaffvgtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsP 262 ld+ele +f +g +n+lGe++ ae hifG+vllndwsardiq+weyvPlGPf++ksf+tt+sP lcl|FitnessBrowser__Burk376:H281DRAFT_04742 212 LDIELETGFVIGGGNALGEPIACTDAEAHIFGMVLLNDWSARDIQQWEYVPLGPFNSKSFTTTISP 277 ****************************************************************** PP TIGR01266 263 wvvsiealePfrvaqlePeqdpkplpylredradtafdielevslkteGlaeaavisrsnakslyw 328 w+v+++alePfrva +P+q+p+pl+ylr+d + afdi lev+l+++G ++a++i+r+n+k +yw lcl|FitnessBrowser__Burk376:H281DRAFT_04742 278 WIVTLDALEPFRVA--QPVQEPQPLAYLRHD-GEHAFDIALEVTLRPQGAKQATTIARTNFKYMYW 340 *************9..9**************.999******************************* PP TIGR01266 329 tlkqqlahhsvnGcnlraGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdev 394 t++qqlahh+v Gcn r Gdl+gsGtisG+ e+++Gsllel+ +Gkk+++l +g tr f+edGde+ lcl|FitnessBrowser__Burk376:H281DRAFT_04742 341 TMAQQLAHHTVGGCNTRVGDLMGSGTISGPTEDSYGSLLELTLNGKKPLELNEGGTRSFIEDGDEL 406 ****************************************************************** PP TIGR01266 395 ilrgvckkeGvrvGfGecaGkvlpa 419 l+g c+ +G+rvGfG c G++lpa lcl|FitnessBrowser__Burk376:H281DRAFT_04742 407 TLSGWCQADGYRVGFGTCVGEILPA 431 ************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (433 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: 10.88 // [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