Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate WP_028999982.1 H537_RS0124705 fumarylacetoacetase
Query= SwissProt::P16930 (419 letters) >NCBI__GCF_000430725.1:WP_028999982.1 Length = 441 Score = 392 bits (1006), Expect = e-113 Identities = 214/420 (50%), Positives = 267/420 (63%), Gaps = 17/420 (4%) Query: 8 EDSDFPIHNLPYGVFSTRG-DPRPRIGVAIGDQILDLSIIKHLFTGPVLSKHQDV-FNQP 65 +D+DFPI NLP G F RG + RIGVAIGDQ+LDL + T H V Sbjct: 21 DDTDFPIQNLPLGAFRRRGSNDALRIGVAIGDQVLDLKLACREGTWTAEVAHALVPLAGG 80 Query: 66 TLNSFMGLGQAAWKEARVFLQNLLSVSQARLRDDTELRKCAFISQASATMHLPATIGDYT 125 LN FM LG AA + R L L+ A+ + L++C + QA A M LP IGDYT Sbjct: 81 DLNGFMALGPAARRAVRTALSAALAEDSAQ---KSALQQC-LVPQAEAEMALPCRIGDYT 136 Query: 126 DFYSSRQHATNVGIMFRDKENALMPNWLHLPVGYHGRASSVVVSGTPIRRPMGQMKPDDS 185 DFY+ HAT VG +FR +N L+PN+ +P+GYHGR SS+VVSGT +RRP+GQ P Sbjct: 137 DFYTGIHHATTVGKLFRP-DNPLLPNYKWVPIGYHGRCSSLVVSGTDLRRPLGQQAPGPD 195 Query: 186 KPPVYGACKLLDMELEMAFFVGPGNRLGEPIPISKAHEHIFGMVLMNDWSARDIQKWEYV 245 P +G CK LD ELE+ VG N LGEP+P+++A EH+FG+VL+NDWSARD+Q WEY Sbjct: 196 GVPGFGPCKRLDYELELGALVGSPNALGEPVPMAQAEEHLFGLVLLNDWSARDVQAWEYQ 255 Query: 246 PLGPFLGKSFGTTVSPWVVPMDALMPFAVP--NPKQDPRPLPYL---CHDEPYTFDINLS 300 PLGPFL K+FG+T+SPWVV M+AL PF P P+ DPRPLPYL + E I Sbjct: 256 PLGPFLSKNFGSTLSPWVVTMEALEPFRAPFKRPEGDPRPLPYLDSIANRERGAIAIRFE 315 Query: 301 VNLKGEGMSQAA----TICKSNFKYMYWTMLQQLTHHSVNGCNLRPGDLLASGTISGPEP 356 V L+ E M + +SNFK YWT+ Q L HH+ NGCNL+PGDLL SGT SGP+ Sbjct: 316 VLLQTEAMRAQGLAPHKLMESNFKDAYWTVAQMLAHHASNGCNLQPGDLLGSGTQSGPDA 375 Query: 357 ENFGSMLELSWKGTKPIDLGNGQTRKFLLDGDEVIITGYCQGDGYR-IGFGQCAGKVLPA 415 GS+LELS G +P+ L G+TR FL DGD V + G C+ G R IGFG+C G +LPA Sbjct: 376 GQGGSLLELSHGGKQPLQLPGGETRLFLQDGDRVFLRGRCEAAGARAIGFGECVGTILPA 435 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: 644 Number of extensions: 40 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: 441 Length adjustment: 32 Effective length of query: 387 Effective length of database: 409 Effective search space: 158283 Effective search space used: 158283 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_028999982.1 H537_RS0124705 (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.17891.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-170 552.8 0.0 2.8e-170 552.6 0.0 1.0 1 lcl|NCBI__GCF_000430725.1:WP_028999982.1 H537_RS0124705 fumarylacetoaceta Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000430725.1:WP_028999982.1 H537_RS0124705 fumarylacetoacetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 552.6 0.0 2.8e-170 2.8e-170 1 419 [. 13 435 .. 13 436 .. 0.96 Alignments for each domain: == domain 1 score: 552.6 bits; conditional E-value: 2.8e-170 TIGR01266 1 sfvavak..nsdfplqnlPyGvfstk.adssrrigvaiGdqildlskiaaaglfeglalkehqevfkes 66 s+v++a+ ++dfp+qnlP+G f + ++ rigvaiGdq+ldl+ + g ++ + +++ + ++ lcl|NCBI__GCF_000430725.1:WP_028999982.1 13 SWVTSANedDTDFPIQNLPLGAFRRRgSNDALRIGVAIGDQVLDLKLACREGTWTA-EVAHALVPLAGG 80 89999987789************9773456789*********************99.6777788899** PP TIGR01266 67 tlnaflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirha 135 ln f+alg +ar++vr l l+e++++ + ++ l++qaea+m lP +iGdytdfy++i+ha lcl|NCBI__GCF_000430725.1:WP_028999982.1 81 DLNGFMALGPAARRAVRTALSAALAEDSAQ----KSALQQCLVPQAEAEMALPCRIGDYTDFYTGIHHA 145 *************************88887....5666789**************************** PP TIGR01266 136 tnvGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelela 204 t vG+lfr +dn+llPnyk++P+gyhGr ss+vvsGt+lrrP Gq + +P fgpck+ld+elel+ lcl|NCBI__GCF_000430725.1:WP_028999982.1 146 TTVGKLFR-PDNPLLPNYKWVPIGYHGRCSSLVVSGTDLRRPLGQQAPGPDGVPGFGPCKRLDYELELG 213 ********.************************************************************ PP TIGR01266 205 ffvgtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePf 273 vg++n+lGe+vp+ +aeeh+fG+vllndwsard+qawey+PlGPfl+k+f++t+sPwvv++ealePf lcl|NCBI__GCF_000430725.1:WP_028999982.1 214 ALVGSPNALGEPVPMAQAEEHLFGLVLLNDWSARDVQAWEYQPLGPFLSKNFGSTLSPWVVTMEALEPF 282 ********************************************************************* PP TIGR01266 274 rvaqlePeqdpkplpylre..dradtafdielevslkteGlae....aavisrsnakslywtlkqqlah 336 r + +Pe+dp+plpyl +r+ a+ i +ev l+te ++ ++++ sn+k+ ywt++q+lah lcl|NCBI__GCF_000430725.1:WP_028999982.1 283 RAPFKRPEGDPRPLPYLDSiaNRERGAIAIRFEVLLQTEAMRAqglaPHKLMESNFKDAYWTVAQMLAH 351 *****************75226799***************99888889********************* PP TIGR01266 337 hsvnGcnlraGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckkeGv 405 h+ nGcnl++GdllgsGt sG++ ++ Gsllels++Gk++++l getr fl+dGd v lrg+c+ G lcl|NCBI__GCF_000430725.1:WP_028999982.1 352 HASNGCNLQPGDLLGSGTQSGPDAGQGGSLLELSHGGKQPLQLPGGETRLFLQDGDRVFLRGRCEAAGA 420 ********************************************************************9 PP TIGR01266 406 r.vGfGecaGkvlpa 419 r +GfGec G++lpa lcl|NCBI__GCF_000430725.1:WP_028999982.1 421 RaIGFGECVGTILPA 435 99***********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (441 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: 7.71 // [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