Align Lmo2663 protein (characterized, see rationale)
to candidate BWI76_RS11535 BWI76_RS11535 putative oxidoreductase, Zn-dependent and NAD(P)-binding protein
Query= uniprot:Q8Y414 (343 letters) >FitnessBrowser__Koxy:BWI76_RS11535 Length = 358 Score = 165 bits (418), Expect = 1e-45 Identities = 107/354 (30%), Positives = 177/354 (50%), Gaps = 15/354 (4%) Query: 1 MKAVVKTNPGYDQMELKDVEEPQVYGDKVKIKVAFTGICGSDIHTFKGEYKNPTTPVTLG 60 MKA+ + + ++ DV EP D V I++ ICG+D+ + + + G Sbjct: 1 MKALARFGKAFGGYKMIDVPEPVCGPDDVVIEIKAAAICGADMKHYNVDSGSDQFNSIRG 60 Query: 61 HEFSGVVVEVGPDVTSIKVGDRVTSETTFETCGECIYCKEHDYNLCSNRRGIGTQAN--- 117 HEF+G +V VG V KVG RV S+ + CG C C++ D+ C+ + +G N Sbjct: 61 HEFAGAIVRVGDKVKDWKVGQRVVSDNSGHVCGVCPACEQGDFLCCAEKVNLGLDNNTWG 120 Query: 118 GSFAEFVLSREESCHV-------LDERISLEAAALTEPLACCVHSALEKTTIRPDDTVLV 170 G F+++ L E + + + E AA+ +P+ S +++ P V+V Sbjct: 121 GGFSKYCLVPGEILKIHRHALWEIPPGVDYEDAAVLDPICNAYKSLAQQSKFLPGQDVVV 180 Query: 171 FGPGPIGLLLAQVVKAQGA-TVIMAGITKD-SDRLRLAKELGMDRIVDTLKEDLAEVVLG 228 FG GP+GL Q+ + GA ++M G+ +D + R +AK LG +V+ ED+ Sbjct: 181 FGTGPLGLFSVQMARIMGAVNIVMVGLEEDVAVRFPIAKALGATAVVNASTEDVVARCQA 240 Query: 229 MTGGYGAERVFDCSGAVPAVNQGLPLTKKKGDFVQVGL-FAEKKNAIDEESIIQREIAYI 287 + G V +CSGA A+ Q + + + G+ V+VG+ F +I++ + + I I Sbjct: 241 ICGKDNLGLVIECSGANIALKQSIEMLRPNGEVVRVGMGFQPLDFSINDITTWNKSI--I 298 Query: 288 GSRSQKPSSWILALDLLANGKIDTDKMITKVYGLDDWREAFEAVMAGNEIKVLV 341 G + +SW A+ LLA+G I MIT GL WRE F+A++ IKV++ Sbjct: 299 GHMAYDSTSWRNAIRLLASGAIKVKPMITHRIGLSQWREGFDAMVDKTAIKVIM 352 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: 336 Number of extensions: 21 Number of successful extensions: 4 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: 358 Length adjustment: 29 Effective length of query: 314 Effective length of database: 329 Effective search space: 103306 Effective search space used: 103306 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