Align D/L-lactic acid transporter; Lactate racemization operon protein LarD; Lactic acid channel (characterized)
to candidate Echvi_1769 Echvi_1769 Glycerol uptake facilitator and related permeases (Major Intrinsic Protein Family)
Query= SwissProt::F9UST3 (238 letters) >FitnessBrowser__Cola:Echvi_1769 Length = 244 Score = 175 bits (444), Expect = 6e-49 Identities = 99/236 (41%), Positives = 135/236 (57%), Gaps = 17/236 (7%) Query: 6 IAEFMGTALMIIFGVGVHCSSVLKGTKYRGSGHIFAITTWGFGISVALFIFG---NVCIN 62 IAEF+GT L+++ G GV + VLK TK SG I T W G+ + + + G +N Sbjct: 5 IAEFIGTGLLLLMGAGVVANVVLKQTKGNNSGWIVITTAWALGVFIGVVVAGPYSGAHLN 64 Query: 63 PAMVLAQCLLGNIAWSLFIPYSVAEVLGGVVGSVIVWIMYADHFKASTDEISPITIRNLF 122 PA+ + + G WSL Y +A++LG GS + W++Y DHF + D P F Sbjct: 65 PAVSVGLAVAGLFEWSLVPGYVLAQILGAGAGSSLAWLIYKDHFDLTDD---PNLKFAPF 121 Query: 123 CTAPAVRNLPRNFFVELFDTFIFISGILAIS--EIKTPGIVPIGVG--------LLVWAI 172 TAPA+RNL NF E+ TF+ I IL + ++ P PIG+G LLVW I Sbjct: 122 ATAPAIRNLSSNFLSEVVGTFVLILVILYSTGANLEDPNNTPIGLGALGALPVALLVWVI 181 Query: 173 GMGLGGPTGFAMNLARDMGPRIAHAILPIANKADSDWQYGIIVPGIAPFVGAAIAA 228 G+ LGG TG+A+N ARD+GPR+AH LPI K SDW Y VP + P +GA++AA Sbjct: 182 GLALGGTTGYAINPARDLGPRLAHQFLPIKGKGSSDWAYS-WVPIVGPLMGASLAA 236 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: 289 Number of extensions: 18 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: 244 Length adjustment: 23 Effective length of query: 215 Effective length of database: 221 Effective search space: 47515 Effective search space used: 47515 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