Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate GFF1748 HP15_1707 short-chain dehydrogenase/reductase SDR
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__Marino:GFF1748 Length = 256 Score = 137 bits (345), Expect = 2e-37 Identities = 100/258 (38%), Positives = 137/258 (53%), Gaps = 19/258 (7%) Query: 3 QRLAGKTALITAAGQGIGLATAELFAREGARVIATDIR-IDGLA-GKPVEARKL------ 54 +RL GK A+IT GIG ATA A EGA V D + +G A K +E R L Sbjct: 2 ERLKGKVAVITGGSVGIGAATALRMAEEGAAVAILDCQDSEGEALAKQLEGRGLKAGYWH 61 Query: 55 -DVRDDAAIK----ALAAEIGAVDVLFNCAGFVHAGNIL-ECSEEDWDFAFDLNVKAMYR 108 DV + +K A+A G VL N AG A E +EE+WD D+NVK ++ Sbjct: 62 CDVSKEQEVKQVLDAVANTFGTPTVLVNNAGIAGANKPTHELTEEEWDHVQDVNVKGVFF 121 Query: 109 MIRAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVR 168 + +P M G GSIIN+SS V P+ Y ASK AV ++K+ A + T +R Sbjct: 122 CTKHAIPHMKKAGVGSIINLSSIYGLVSA-PDIPPYHASKGAVRLMSKTDALLYATENIR 180 Query: 169 CNAICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGS 228 CN+I PG + +P +E A + G + + A A P+G +G+P++IA A+YL S Sbjct: 181 CNSIHPGFIWTPLVE----AHLKTTGQDPEEAKKATAAMHPVGHMGEPDDIAWGAVYLAS 236 Query: 229 DESSFTTGHAHVIDGGWS 246 DES F TG VIDGG++ Sbjct: 237 DESKFVTGSELVIDGGYT 254 Lambda K H 0.320 0.133 0.381 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: 148 Number of extensions: 10 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: 247 Length of database: 256 Length adjustment: 24 Effective length of query: 223 Effective length of database: 232 Effective search space: 51736 Effective search space used: 51736 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 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