Align Lactate utilization protein A (characterized)
to candidate 353981 BT4455 oxidoreductase, putative glycolate oxidase (NCBI ptt file)
Query= SwissProt::Q81GA5 (239 letters) >FitnessBrowser__Btheta:353981 Length = 246 Score = 159 bits (401), Expect = 6e-44 Identities = 87/250 (34%), Positives = 139/250 (55%), Gaps = 15/250 (6%) Query: 1 MKVTLFVTCLVDMFETNVGKATVEVLERLGCEIEFPEAQVCCGQPAYNSGHVEAAKEAMK 60 MKV LF+ C ++ NVG A+ ++L+ LG ++++P Q CCGQP N+G + + + Sbjct: 1 MKVGLFIPCYINAIYPNVGVASYKLLKSLGVDVDYPLDQTCCGQPMANAGFEDESMKLAL 60 Query: 61 HMIETFEDAEYIVTPSGSCATMFHE-YPHVFKDDPKWAKRAQKVADKTYEFTQFIVDVLK 119 + F + +YIV PS SC E +P + + + + A K+ Y+ +FI DVLK Sbjct: 61 RFDDLFREYDYIVGPSASCVAFVKENHPGILEKEGHVCQSAGKI----YDLCEFIHDVLK 116 Query: 120 VTDVGASLPGIATIHKSCHMTRMLGVKEAPGI----------LLSNVKGLTVRDLPNVQN 169 T + A P +IH SCH R L + + LL V+G+ V + ++ Sbjct: 117 PTKIPARFPHKVSIHNSCHGVRELLISAPSELNIPYYNKLRDLLDMVEGIEVFEPSHIDE 176 Query: 170 CCGFGGTFSVKMTPISEQMVDEKVDSVMETGADYLIGADCGCLLNIGGRIERLGKEVKVM 229 CCGFGG F+V+ +S M +KV M TGA+Y++GAD CL+++ G I+R ++++ Sbjct: 177 CCGFGGMFAVEEQAVSVCMGRDKVKDHMATGAEYIVGADSSCLMHMQGVIKREHLPIQII 236 Query: 230 HIAEVLNSRS 239 HI E+L S+S Sbjct: 237 HIVEILASQS 246 Lambda K H 0.320 0.135 0.407 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: 220 Number of extensions: 10 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: 239 Length of database: 246 Length adjustment: 23 Effective length of query: 216 Effective length of database: 223 Effective search space: 48168 Effective search space used: 48168 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