Align Lactaldehyde reductase (characterized, see rationale)
to candidate 353293 BT3767 lactaldehyde reductase (NCBI ptt file)
Query= uniprot:Q8A199 (384 letters) >FitnessBrowser__Btheta:353293 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.879.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.77 // [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