Align Lactaldehyde reductase (characterized, see rationale)
to candidate BPHYT_RS20205 BPHYT_RS20205 alcohol dehydrogenase
Query= uniprot:Q8A199 (384 letters) >FitnessBrowser__BFirm:BPHYT_RS20205 Length = 386 Score = 194 bits (493), Expect = 4e-54 Identities = 124/375 (33%), Positives = 201/375 (53%), Gaps = 6/375 (1%) Query: 12 FGAGCRSVIAVEAARRGFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPYELYSDVKANPT 71 FGA R + A + VTD L + G+ + + + DV A+P Sbjct: 16 FGAARRLGALLRAQFPALSRVCVVTDGFLHRSGLLNPALADLATHGWDATVIDDVIADPP 75 Query: 72 IANVQNGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNNPDFADVKSLEGVADTKHKAV 131 V + + +GA+ ++ LGGGSS+D AK I ++ A + + GV + Sbjct: 76 EHIVLEATSRARTAGAEIVLGLGGGSSMDVAKLIAVLAPQQQQA-LSEMYGVNKITVARL 134 Query: 132 PTFALPTTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIVDPELMYSMPKGLTAAT 191 P +PTTAGT +EVT ++ +A KKM V P I +AI+D EL +P TAAT Sbjct: 135 PLVQMPTTAGTGSEVTAVSIVTVGEA-KKMGVVAPQLIADLAILDAELTLGLPVAATAAT 193 Query: 192 GMDALTHAIESYITPGAW-AMSDMFELKAIEMIAQNLKAAVDNGKDTVAREAMSQAQYIA 250 G+DA+ HAIE+Y + +SD+ +KA++++++NL A +NG D AREAM A Sbjct: 194 GVDAMVHAIEAYTSAHLKNPVSDLLAVKALDLLSRNLLPACENGDDRAAREAMLLGATFA 253 Query: 251 GMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNAESPAAPKYIHIAKAMGV 310 G F+N + VH++A+P+G Y PHG++NAL+LP+V+ +NA++ AAP Y +A+ + Sbjct: 254 GQAFANSPVAAVHALAYPIGGIYHVPHGLSNALVLPHVLRFNADA-AAPLYAELAEVVVP 312 Query: 311 NTDGMTETEGVKAAIEAVKALSLSIGIPQKLHEINVKEEDIPALAV-AAFNDVCTGGNPR 369 G E++ +A IE ++ + + IP +L ++ +++ + +A A NPR Sbjct: 313 GVTGSDESK-TQALIERLEQMIAATAIPARLRDVGIEQSGLERMASDAMLQTRLLVNNPR 371 Query: 370 PTSVAEIEVLYRKAF 384 P + A+ +Y AF Sbjct: 372 PVTEADALAIYTAAF 386 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: 354 Number of extensions: 19 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: 384 Length of database: 386 Length adjustment: 30 Effective length of query: 354 Effective length of database: 356 Effective search space: 126024 Effective search space used: 126024 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)
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