Align D/L-lactic acid transporter; Lactate racemization operon protein LarD; Lactic acid channel (characterized)
to candidate PP_1076 PP_1076 aquaglyceroporin
Query= SwissProt::F9UST3 (238 letters) >FitnessBrowser__Putida:PP_1076 Length = 283 Score = 97.1 bits (240), Expect = 3e-25 Identities = 75/253 (29%), Positives = 123/253 (48%), Gaps = 22/253 (8%) Query: 4 QLIAEFMGTALMIIFGVGVHCSSVLKGTKYRGSGHIFAITTWGFGISVALFIFGNVC--- 60 Q +AEF+GTAL+I FG G + + G + G I I WG G+S+A+++ + Sbjct: 13 QCLAEFLGTALLIFFGTGCVAALKVAGASF-GLWEISII--WGVGVSMAIYLTAGISGAH 69 Query: 61 INPAMVLAQCLLGNIAWSLFIPYSVAEVLGGVVGSVIVWIMYADHF-------KASTDEI 113 +NPA+ +A L Y +A+V G G+ +V+ +Y++ F Sbjct: 70 LNPAVSIALTLFAGFDKRKLPFYMLAQVCGAFCGAALVYTLYSNLFFDFEQAHAMLRGSE 129 Query: 114 SPITIRNLFCTAPAVR-NLPRNFFVELFDTFIFISGILAISE----IKTPGIVPIGVGLL 168 + + ++F T P + + F VE+ T I ++ I+A+++ + + P+ +GLL Sbjct: 130 GSLELASVFSTYPHPSLSTSQAFLVEVVITAILMAVIMALTDDNNGLPRGAMAPLLIGLL 189 Query: 169 VWAIGMGLGGPTGFAMNLARDMGPRIAHAIL---PIANKADSDWQYGIIVPGIAPFVGAA 225 + IG +G TGFAMN ARD GP++ + IA D Y +VP AP +GA Sbjct: 190 IAVIGSAMGPLTGFAMNPARDFGPKLMTFLAGWGEIAFTGGRDIPY-FLVPVFAPILGAC 248 Query: 226 IAAWFMHGFFGIN 238 + A G N Sbjct: 249 LGAASYRGLIARN 261 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: 223 Number of extensions: 13 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: 283 Length adjustment: 24 Effective length of query: 214 Effective length of database: 259 Effective search space: 55426 Effective search space used: 55426 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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