Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate 3610430 Dshi_3811 fumarylacetoacetase (RefSeq)
Query= SwissProt::P16930 (419 letters) >FitnessBrowser__Dino:3610430 Length = 413 Score = 404 bits (1037), Expect = e-117 Identities = 210/416 (50%), Positives = 272/416 (65%), Gaps = 15/416 (3%) Query: 2 SFIPVAED--SDFPIHNLPYGVFSTRGDPRPRIGVAIGDQILDLSIIKHLFTGPVLSKHQ 59 S++P A D FP++NL +GVFST GD PR VAIGD++LDL+ ++ +L H Sbjct: 7 SWVPGANDPAGAFPLNNLAFGVFST-GDG-PRCAVAIGDKVLDLAALQ---AAGLLPDHG 61 Query: 60 DVFNQPTLNSFMGLGQAAWKEARVFLQNLLSVSQARLRDDTELRKCAFISQASATMHLPA 119 F+ P L++FMG GQ AW+ R L LL R +T + A +A +HLP Sbjct: 62 --FDAPALDTFMGRGQPAWQAVREALTELL-----RAGAETAPVRAALHDRAGVRLHLPF 114 Query: 120 TIGDYTDFYSSRQHATNVGIMFRDKENALMPNWLHLPVGYHGRASSVVVSGTPIRRPMGQ 179 T+ ++TDFY+ RQHA NVG +FRD NAL PNWLH+P+GY+GRAS+VVVSGTPI RP GQ Sbjct: 115 TLAEFTDFYAGRQHAFNVGSLFRDPANALPPNWLHMPIGYNGRASTVVVSGTPIHRPAGQ 174 Query: 180 MKPDDSKPPVYGACKLLDMELEMAFFVGPGNRLGEPIPISKAHEHIFGMVLMNDWSARDI 239 +K P +G C+ LD ELE+ VG +++G P+ + +A E IFG VL+NDWSARDI Sbjct: 175 IKDPSDPMPRFGPCERLDFELELGAVVGTPSQMGVPVTVDEADEMIFGYVLLNDWSARDI 234 Query: 240 QKWEYVPLGPFLGKSFGTTVSPWVVPMDALMPFAVPNPKQDPRPLPYLCHDEPYTFDINL 299 Q WEYVPLGPF GK+F TT+SPWVVP AL PF P ++ LP+L P DI+L Sbjct: 235 QAWEYVPLGPFQGKAFATTISPWVVPRAALAPFRCGPPVREVPLLPHLRDTGPMFHDIDL 294 Query: 300 SVNLKGEGMSQAATICKSNFKYMYWTMLQQLTHHSVNGCNLRPGDLLASGTISGPEPENF 359 +V L G +C++N +Y++ Q L HHS +GC +R GDLL SGTISGPE F Sbjct: 295 AVTLAPPG-GAPTEVCRTNSNALYYSAAQLLAHHSTSGCAMRTGDLLGSGTISGPEKGMF 353 Query: 360 GSMLELSWKGTKPIDLGNGQTRKFLLDGDEVIITGYCQGDGYRIGFGQCAGKVLPA 415 GS+LE++W G P+ L G TR+FL DGD V + G +GDGYRIGFG C G +LPA Sbjct: 354 GSLLEITWGGRDPVALAGGATRRFLADGDTVTLKGEARGDGYRIGFGTCTGTILPA 409 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: 612 Number of extensions: 20 Number of successful extensions: 5 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: 413 Length adjustment: 31 Effective length of query: 388 Effective length of database: 382 Effective search space: 148216 Effective search space used: 148216 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: 50 (23.9 bits)
Align candidate 3610430 Dshi_3811 (fumarylacetoacetase (RefSeq))
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.6274.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-157 508.8 0.0 6.3e-157 508.6 0.0 1.0 1 lcl|FitnessBrowser__Dino:3610430 Dshi_3811 fumarylacetoacetase (R Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3610430 Dshi_3811 fumarylacetoacetase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 508.6 0.0 6.3e-157 6.3e-157 1 419 [. 7 409 .. 7 410 .. 0.97 Alignments for each domain: == domain 1 score: 508.6 bits; conditional E-value: 6.3e-157 TIGR01266 1 sfvavak..nsdfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevfkestlnaflalg 75 s+v+ a+ fpl+nl +Gvfs ++ +r++vaiGd++ldl++++aagl+ + + f+ +l++f++ g lcl|FitnessBrowser__Dino:3610430 7 SWVPGANdpAGAFPLNNLAFGVFS--TGDGPRCAVAIGDKVLDLAALQAAGLLPD-------HGFDAPALDTFMGRG 74 789888844468************..56789********************9988.......89************* PP TIGR01266 76 rparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhatnvGilfrgkdnallPn 152 +pa+++vre l +ll + ae+ a + al+ +a ++ hlP ++ ++tdfy++++ha nvG lfr + nal Pn lcl|FitnessBrowser__Dino:3610430 75 QPAWQAVREALTELLRAGAET-----APVRAALHDRAGVRLHLPFTLAEFTDFYAGRQHAFNVGSLFRDPANALPPN 146 ***************966655.....5566799******************************************** PP TIGR01266 153 ykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaffvgtenelGeavpiekaeehifGv 229 + h+P+gy Gras+vvvsGt+++rP Gqik + +P fgpc++ld+elel+ vgt+ ++G +v ++ a+e ifG lcl|FitnessBrowser__Dino:3610430 147 WLHMPIGYNGRASTVVVSGTPIHRPAGQIKDPSDPMPRFGPCERLDFELELGAVVGTPSQMGVPVTVDEADEMIFGY 223 ***************************************************************************** PP TIGR01266 230 vllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfrvaqlePeqdpkplpylredradtafdielevs 306 vllndwsardiqaweyvPlGPf +k+fatt+sPwvv+ al Pfr P+++ +lp+lr+ ++ +di+l+v+ lcl|FitnessBrowser__Dino:3610430 224 VLLNDWSARDIQAWEYVPLGPFQGKAFATTISPWVVPRAALAPFRCG--PPVREVPLLPHLRDT-GPMFHDIDLAVT 297 *********************************************99..888888899****99.9*********** PP TIGR01266 307 lkteGlaeaavisrsnakslywtlkqqlahhsvnGcnlraGdllgsGtisGkeeeafGsllelsakGkkevkladge 383 l + G + ++ ++r+n+ ly++ +q lahhs +Gc +r+GdllgsGtisG+e++ fGslle++++G+++v la g lcl|FitnessBrowser__Dino:3610430 298 LAPPG-GAPTEVCRTNSNALYYSAAQLLAHHSTSGCAMRTGDLLGSGTISGPEKGMFGSLLEITWGGRDPVALAGGA 373 *****.99********************************************************************* PP TIGR01266 384 trkfledGdevilrgvckkeGvrvGfGecaGkvlpa 419 tr+fl dGd+v l+g ++ +G+r+GfG c+G++lpa lcl|FitnessBrowser__Dino:3610430 374 TRRFLADGDTVTLKGEARGDGYRIGFGTCTGTILPA 409 **********************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (413 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: 11.56 // [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