Align Lactaldehyde reductase (characterized, see rationale)
to candidate 353293 BT3767 lactaldehyde reductase (NCBI ptt file)
Query= uniprot:Q8A199 (384 letters) >lcl|FitnessBrowser__Btheta:353293 BT3767 lactaldehyde reductase (NCBI ptt file) Length = 384 Score = 755 bits (1950), Expect = 0.0 Identities = 384/384 (100%), Positives = 384/384 (100%) Query: 1 MNRIILNETSYFGAGCRSVIAVEAARRGFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPY 60 MNRIILNETSYFGAGCRSVIAVEAARRGFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPY Sbjct: 1 MNRIILNETSYFGAGCRSVIAVEAARRGFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPY 60 Query: 61 ELYSDVKANPTIANVQNGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNNPDFADVKSL 120 ELYSDVKANPTIANVQNGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNNPDFADVKSL Sbjct: 61 ELYSDVKANPTIANVQNGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNNPDFADVKSL 120 Query: 121 EGVADTKHKAVPTFALPTTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIVDPELM 180 EGVADTKHKAVPTFALPTTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIVDPELM Sbjct: 121 EGVADTKHKAVPTFALPTTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIVDPELM 180 Query: 181 YSMPKGLTAATGMDALTHAIESYITPGAWAMSDMFELKAIEMIAQNLKAAVDNGKDTVAR 240 YSMPKGLTAATGMDALTHAIESYITPGAWAMSDMFELKAIEMIAQNLKAAVDNGKDTVAR Sbjct: 181 YSMPKGLTAATGMDALTHAIESYITPGAWAMSDMFELKAIEMIAQNLKAAVDNGKDTVAR 240 Query: 241 EAMSQAQYIAGMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNAESPAAPK 300 EAMSQAQYIAGMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNAESPAAPK Sbjct: 241 EAMSQAQYIAGMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNAESPAAPK 300 Query: 301 YIHIAKAMGVNTDGMTETEGVKAAIEAVKALSLSIGIPQKLHEINVKEEDIPALAVAAFN 360 YIHIAKAMGVNTDGMTETEGVKAAIEAVKALSLSIGIPQKLHEINVKEEDIPALAVAAFN Sbjct: 301 YIHIAKAMGVNTDGMTETEGVKAAIEAVKALSLSIGIPQKLHEINVKEEDIPALAVAAFN 360 Query: 361 DVCTGGNPRPTSVAEIEVLYRKAF 384 DVCTGGNPRPTSVAEIEVLYRKAF Sbjct: 361 DVCTGGNPRPTSVAEIEVLYRKAF 384 Lambda K H 0.317 0.133 0.379 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: 678 Number of extensions: 11 Number of successful extensions: 1 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: 384 Length of database: 384 Length adjustment: 30 Effective length of query: 354 Effective length of database: 354 Effective search space: 125316 Effective search space used: 125316 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate 353293 BT3767 (lactaldehyde reductase (NCBI ptt file))
to HMM TIGR02638 (fucO: lactaldehyde reductase (EC 1.1.1.77))
# 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/TIGR02638.hmm # target sequence database: /tmp/gapView.17960.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02638 [M=379] Accession: TIGR02638 Description: lactal_redase: lactaldehyde reductase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-200 651.9 11.0 1.5e-200 651.7 11.0 1.0 1 lcl|FitnessBrowser__Btheta:353293 BT3767 lactaldehyde reductase (N Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:353293 BT3767 lactaldehyde reductase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 651.7 11.0 1.5e-200 1.5e-200 1 379 [] 1 380 [. 1 380 [. 0.99 Alignments for each domain: == domain 1 score: 651.7 bits; conditional E-value: 1.5e-200 TIGR02638 1 snrlilnevsyfGaGaiedivkevkrrgfkkalvvtdkdliklgvvdkvlelldeaklayelfdevvpnPtvevvk 76 +nr+ilne+syfGaG++++i+ e +rrgfkka++vtdkdlik+gv++++++++d+++++yel+++v++nPt+++v+ lcl|FitnessBrowser__Btheta:353293 1 MNRIILNETSYFGAGCRSVIAVEAARRGFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPYELYSDVKANPTIANVQ 76 69************************************************************************** PP TIGR02638 77 eGlaafkesgadyliaiGGGspidtakaigiivnnPefadvvsleGvadtkkkavpiiaipttaGtaaevtinyvi 152 +G+aa+k+sgad+++a+GGGs+idtak+igi+vnnP+fadv+sleGvadtk+kavp++a+pttaGtaaevtinyvi lcl|FitnessBrowser__Btheta:353293 77 NGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNNPDFADVKSLEGVADTKHKAVPTFALPTTAGTAAEVTINYVI 152 **************************************************************************** PP TIGR02638 153 tdeekkrklvivdpkdiPavavvdaelmlslPksltaatGldalthaiegyitkgaweltdalelkaieliaralk 228 +de++++k+v+vdp+diPava+vd+elm+s+Pk ltaatG+dalthaie+yit+gaw+++d++elkaie+ia++lk lcl|FitnessBrowser__Btheta:353293 153 IDEDARKKMVCVDPNDIPAVAIVDPELMYSMPKGLTAATGMDALTHAIESYITPGAWAMSDMFELKAIEMIAQNLK 228 **************************************************************************** PP TIGR02638 229 savedgkdkeareelalgqyvaGmafsnvGlGlvhglahplgalydlPhGvanaillPivmefnae.kagekyrei 303 +av++gkd+ are+++++qy+aGm+fsnvGlG+vh++ahplga+yd+PhGvana+llP+vme+nae a+ ky++i lcl|FitnessBrowser__Btheta:353293 229 AAVDNGKDTVAREAMSQAQYIAGMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNAEsPAAPKYIHI 304 *****************************************************************967999***** PP TIGR02638 304 akamgvkteelseeeareaaveavktlskrvgiPeklselgvkeediealaeaaladvCtggnPreataeeieely 379 akamgv+t++++e+e ++aa+eavk+ls ++giP+kl+e++vkeedi+ala aa++dvCtggnPr+++++eie ly lcl|FitnessBrowser__Btheta:353293 305 AKAMGVNTDGMTETEGVKAAIEAVKALSLSIGIPQKLHEINVKEEDIPALAVAAFNDVCTGGNPRPTSVAEIEVLY 380 *************************************************************************999 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (379 nodes) Target sequences: 1 (384 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: 6.98 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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