Align Lmo2663 protein (characterized, see rationale)
to candidate WP_017549841.1 C792_RS0112730 zinc-binding alcohol dehydrogenase family protein
Query= uniprot:Q8Y414 (343 letters) >NCBI__GCF_000330705.1:WP_017549841.1 Length = 338 Score = 163 bits (412), Expect = 7e-45 Identities = 107/330 (32%), Positives = 167/330 (50%), Gaps = 9/330 (2%) Query: 1 MKAVVKTNPGYDQMELKDVEEPQVY-GDKVKIKVAFTGICGSDIHTFKGEYKNPTTPVTL 59 MKA+ PG Q+ + ++E+P + GD+V +K+ GICGSD+H + G + P + Sbjct: 1 MKAIQVEKPG--QLNIVELEKPVIENGDEVIVKIKNVGICGSDVHIYHGSNPFTSYPRVI 58 Query: 60 GHEFSGVVVEVGPDVTSIKVGDRVTSETTFETCGECIYCKEHDYNLCSNRRGIGTQANGS 119 GHE SG+V +VG VTS+ GD V E CGEC C+ N+C + G +G Sbjct: 59 GHEVSGIVEQVGEAVTSLAPGDLVALE-PITYCGECYACRNGQPNVCDSLEVFGVHRDGG 117 Query: 120 FAEFVLSREESCHVLDERISLEAAALTEPLACCVHSALEKTTIRPDDTVLVFGPGPIGLL 179 AE++ + E + H + +S EAAAL EP+ A + +R DTV V G GP G+ Sbjct: 118 MAEYLKADENNWHKVPGNVSEEAAALMEPMTIGA-QATYRGDVREGDTVFVIGAGPTGIA 176 Query: 180 LAQVVKAQGATVIMAGITKDSDRLRLAKELGMDRIVDTLKEDLAEVVLGMTGGYGAERVF 239 K +GA V ++ + +RL AK +G D + + E + +T G A V Sbjct: 177 CLLQAKQRGAKVFISDF--NQNRLDYAKSIGADATIQPDGVHVEEEINRLTNGELANVVI 234 Query: 240 DCSGAVPAVNQGLPLTKKKGDFVQVGLFAEKKNAIDEESIIQREIAYIGSRSQKPSSWIL 299 D G Q + L G V +G F E+ ++I + ++E+ GSR Q + Sbjct: 235 DAVGLPQTFQQAVELASIAGRVVTLG-FNEQPSSIPSLLLTKKELKVAGSRLQ-THQFPK 292 Query: 300 ALDLLANGKIDTDKMITKVYGLDDWREAFE 329 +D + G+ID ++I++ Y +D +AFE Sbjct: 293 VIDQVGRGEIDPTQIISQRYSMDQIHDAFE 322 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: 312 Number of extensions: 17 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: 343 Length of database: 338 Length adjustment: 28 Effective length of query: 315 Effective length of database: 310 Effective search space: 97650 Effective search space used: 97650 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 24 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