Align Lmo2663 protein (characterized, see rationale)
to candidate HSERO_RS02795 HSERO_RS02795 alcohol dehydrogenase
Query= uniprot:Q8Y414 (343 letters) >FitnessBrowser__HerbieS:HSERO_RS02795 Length = 386 Score = 99.8 bits (247), Expect = 1e-25 Identities = 76/257 (29%), Positives = 116/257 (45%), Gaps = 31/257 (12%) Query: 14 MELKDVEEPQVY-GDKVKIKVAFTGICGSDIHTFKGEYKNPTTPVTLGHEFSGVVVEVGP 72 + ++ V +P + D V +KV T ICGSD+H ++G+ LGHEF GVVVE GP Sbjct: 12 VRVETVPDPIIQEADDVILKVTATAICGSDLHLYRGKIPATKAGDILGHEFMGVVVEAGP 71 Query: 73 DVTSIKVGDRVTSETTFETCGECIYCKEHDYNLCS----------NRRGIGTQA------ 116 + +K GDRV CG+C +C +H Y C N +GI + A Sbjct: 72 AIKRLKKGDRVVVPFVI-ACGQCFFCDQHLYAACETTNPDRGALMNAKGIRSGAAMFGYS 130 Query: 117 ------NGSFAEFVLSREESCHV----LDERISLEAAALTEPLACCVHSALEKTTIRPDD 166 G AE+V R V +D ++ E + + A++ +R Sbjct: 131 HLYGGMPGGQAEYV--RVPKADVGPIRIDSALADEQVLFLSDILPTGYQAVKNAGVREGS 188 Query: 167 TVLVFGPGPIGLLLAQVVKAQGATVIMAGITKDSDRLRLAKELGMDRIVDTLKEDLAEVV 226 +V ++G GP+G + A + GA I + + RLR A+E V+ + D AE + Sbjct: 189 SVAIYGAGPVGQMAAASARMLGAERIFM-VDHHAYRLRFAQEQYDVIPVNFDQVDPAEYI 247 Query: 227 LGMTGGYGAERVFDCSG 243 + T G G + V D G Sbjct: 248 IANTAGRGVDGVIDAVG 264 Lambda K H 0.317 0.135 0.392 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: 299 Number of extensions: 16 Number of successful extensions: 3 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: 343 Length of database: 386 Length adjustment: 29 Effective length of query: 314 Effective length of database: 357 Effective search space: 112098 Effective search space used: 112098 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 (21.6 bits) S2: 49 (23.5 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