Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate BPHYT_RS11790 BPHYT_RS11790 fumarylacetoacetase
Query= BRENDA::Q8RW90 (421 letters) >FitnessBrowser__BFirm:BPHYT_RS11790 Length = 440 Score = 335 bits (859), Expect = 2e-96 Identities = 185/416 (44%), Positives = 253/416 (60%), Gaps = 16/416 (3%) Query: 16 FPIQNLPYGVFKPE-SNSTPRPAVAIGDLVLDLSAISEAGLFDGLILKDADCFLQPNLNK 74 FPIQNLP+ VF+ S+ R AVAIGD V+D++A + +G+ + A QP LN+ Sbjct: 27 FPIQNLPFSVFRRRHSDEAFRGAVAIGDQVIDIAAWASRAGLNGIAGEGARVCAQPVLNE 86 Query: 75 FLAMGRPAWKEARSTLQRILSSNEPILRDNDVLRRKSFHQMSKVEMIVPMVIGDYTDFFA 134 F +MG AW+ R L L P D+ S+VE +P IGDYTDF+ Sbjct: 87 FFSMGPSAWRAVRHALFAALHERAP--SDDRAALEACLIPQSEVEYGLPAQIGDYTDFYT 144 Query: 135 SMHHAKNCGLMFRGPENAINPNWFRLPIAYHGRASSIVISGTDIIRPRGQGHPQGNSEPY 194 S+HHA N + + + N+ +PIAYHGR SSI +SG RP GQ G P Sbjct: 145 SIHHATNISKLLG--LSGVGANFKSIPIAYHGRVSSIGLSGQRFRRPAGQIMLPGEDAPI 202 Query: 195 FGPSKKLDFELEMAAVVGPGNELGKPIDVNNAADHIFGLLLMNDWSARDIQAWEYVPLGP 254 F PS+KLD+ELE+ +G GN G+PI ++ A H+FGL L+NDWSARDIQAWE PLGP Sbjct: 203 FSPSRKLDYELELGIYIGQGNAAGEPIALDQADSHVFGLCLLNDWSARDIQAWEMQPLGP 262 Query: 255 FLGKSFGTTISPWIVTLDALEPFGCQAPK--QDPPPLPYL-AEKESVN--YDISLEVQLK 309 FL K+F TTISPWIVT++AL PF P+ D PLPYL +++ S DI LEV ++ Sbjct: 263 FLAKNFATTISPWIVTMEALAPFRLPLPRPHTDGKPLPYLDSDRNSTTGAIDIQLEVCIE 322 Query: 310 PS----GRDDSCVITKSNFQNLYWTITQQLAHHTVNGCNLRPGDLLGTGTISGPEPDSYG 365 S G + ++ ++F++ YW+I Q +AHH GCNLR GDLLG+GTISGP G Sbjct: 323 TSRHQAGNLPAAQLSLTSFRHQYWSIAQMVAHHAAGGCNLRAGDLLGSGTISGPGQSEAG 382 Query: 366 CLLELTWNGQKPLSLN-GTTQTFLEDGDQVTFSGVCKGDGY-NVGFGTCTGKIVPS 419 L+EL N +P++LN G ++++EDGD + G C+ G+ +GFG G+++P+ Sbjct: 383 ALMELARNASEPVTLNTGEKRSYVEDGDAIILRGYCEKAGFARIGFGESRGEVLPA 438 Lambda K H 0.319 0.139 0.434 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: 560 Number of extensions: 18 Number of successful extensions: 6 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: 421 Length of database: 440 Length adjustment: 32 Effective length of query: 389 Effective length of database: 408 Effective search space: 158712 Effective search space used: 158712 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 (21.7 bits) S2: 51 (24.3 bits)
Align candidate BPHYT_RS11790 BPHYT_RS11790 (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.7147.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-149 482.6 0.0 5.7e-149 482.4 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS11790 BPHYT_RS11790 fumarylacetoacetas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS11790 BPHYT_RS11790 fumarylacetoacetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 482.4 0.0 5.7e-149 5.7e-149 1 419 [. 15 438 .. 15 439 .. 0.95 Alignments for each domain: == domain 1 score: 482.4 bits; conditional E-value: 5.7e-149 TIGR01266 1 sfvavak..nsdfplqnlPyGvfstk.adssrrigvaiGdqildlskiaaaglfeglalkehqevfkest 67 s+v++a+ +dfp+qnlP+ vf + +d r +vaiGdq++d+++ a+ ++++g ++e + v + lcl|FitnessBrowser__BFirm:BPHYT_RS11790 15 SWVESANapTCDFPIQNLPFSVFRRRhSDEAFRGAVAIGDQVIDIAAWASRAGLNG-IAGEGARVCAQPV 83 89999997789************976245667899***************9*****.88999******** PP TIGR01266 68 lnaflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhatn 137 ln f+++g +a+++vr+ l l e a d++a + l++q+e++ lPaqiGdytdfy+si+hatn lcl|FitnessBrowser__BFirm:BPHYT_RS11790 84 LNEFFSMGPSAWRAVRHALFAALHERAPS--DDRAALEACLIPQSEVEYGLPAQIGDYTDFYTSIHHATN 151 *********************99966665..88888899******************************* PP TIGR01266 138 vGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaffv 207 + +l+ + n+k +P++yhGr ss+ sG rrP Gqi ++ + P+f+p++kld+elel++++ lcl|FitnessBrowser__BFirm:BPHYT_RS11790 152 ISKLLG--LSGVGANFKSIPIAYHGRVSSIGLSGQRFRRPAGQIMLPGEDAPIFSPSRKLDYELELGIYI 219 ****98..577899******************************************************** PP TIGR01266 208 gtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfrvaq 277 g++n+ Ge++ +++a+ h+fG++llndwsardiqawe +PlGPflak+fatt+sPw+v++eal Pfr + lcl|FitnessBrowser__BFirm:BPHYT_RS11790 220 GQGNAAGEPIALDQADSHVFGLCLLNDWSARDIQAWEMQPLGPFLAKNFATTISPWIVTMEALAPFRLPL 289 ********************************************************************** PP TIGR01266 278 lePeqdpkplpylredr..adtafdielevslkteGlae....aavisrsnakslywtlkqqlahhsvnG 341 +P+ d kplpyl dr a+di+lev ++t + aa++s + +++ yw+++q++ahh+ G lcl|FitnessBrowser__BFirm:BPHYT_RS11790 290 PRPHTDGKPLPYLDSDRnsTTGAIDIQLEVCIETSRHQAgnlpAAQLSLTSFRHQYWSIAQMVAHHAAGG 359 **************9995456689******998765444445599************************* PP TIGR01266 342 cnlraGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckkeGvr.vGfG 410 cnlraGdllgsGtisG+ + + G+l+el+ + +++v l ge+r ++edGd +ilrg c+k G +GfG lcl|FitnessBrowser__BFirm:BPHYT_RS11790 360 CNLRAGDLLGSGTISGPGQSEAGALMELARNASEPVTLNTGEKRSYVEDGDAIILRGYCEKAGFArIGFG 429 ***************************************************************877**** PP TIGR01266 411 ecaGkvlpa 419 e +G+vlpa lcl|FitnessBrowser__BFirm:BPHYT_RS11790 430 ESRGEVLPA 438 ********8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (440 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: 10.73 // [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