Align D/L-lactic acid transporter; Lactate racemization operon protein LarD; Lactic acid channel (characterized)
to candidate H281DRAFT_04230 H281DRAFT_04230 glycerol uptake facilitator protein
Query= SwissProt::F9UST3 (238 letters) >FitnessBrowser__Burk376:H281DRAFT_04230 Length = 237 Score = 176 bits (446), Expect = 4e-49 Identities = 89/228 (39%), Positives = 138/228 (60%), Gaps = 9/228 (3%) Query: 6 IAEFMGTALMIIFGVGVHCSSVLKGTKYRGSGHIFAITTWGFGISVALFI---FGNVCIN 62 IAEF+GTAL+++ G G + +L TK +G+ I + W + +A+++ + +N Sbjct: 5 IAEFIGTALVVLLGDGAVANVLLARTKGKGADLIVIVMGWAMAVFIAVYVTASYSGAHLN 64 Query: 63 PAMVLAQCLLGNIAWSLFIPYSVAEVLGGVVGSVIVWIMYADHFKASTDEISPITIRNLF 122 P + ++ L G AW+ Y A++LGG+ G+++VW+ Y HF D + + F Sbjct: 65 PVVTISLALAGKFAWAKVPGYIAAQMLGGMAGALLVWVAYRQHFAKEGDADVKLGV---F 121 Query: 123 CTAPAVRNLPRNFFVELFDTFIFISGILAIS--EIKTPGIVPIGVGLLVWAIGMGLGGPT 180 CTAPA+R++P N E+ TF+ I G+L ++ ++ + + VGLLV IG+ LGGPT Sbjct: 122 CTAPAIRSVPHNLLTEMIATFVLILGVLYLASPQVGLGALDALPVGLLVLGIGISLGGPT 181 Query: 181 GFAMNLARDMGPRIAHAILPIANKADSDWQYGIIVPGIAPFVGAAIAA 228 G+AM+ ARD+ PR+ HA+LPI K DSDW+Y I P P VG A+AA Sbjct: 182 GYAMSPARDLSPRLMHALLPIPGKRDSDWRYAWI-PVCGPLVGGAVAA 228 Lambda K H 0.330 0.145 0.470 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: 215 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: 238 Length of database: 237 Length adjustment: 23 Effective length of query: 215 Effective length of database: 214 Effective search space: 46010 Effective search space used: 46010 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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