Align L-lactate transporter; SfMCT (characterized)
to candidate WP_013450393.1 CALNI_RS01295 MFS transporter
Query= SwissProt::A0LNN5 (412 letters) >NCBI__GCF_000183405.1:WP_013450393.1 Length = 380 Score = 168 bits (425), Expect = 3e-46 Identities = 117/382 (30%), Positives = 180/382 (47%), Gaps = 36/382 (9%) Query: 29 YAWSVFIKPLNAEFGWSRAEIAMAFAICCLIFGLMTFPAGRLSDKMGPRKVVMTGGVLLA 88 Y+WSV++K + A S+A+ + F++ IF +G++ K+GP+ + GG L Sbjct: 20 YSWSVYVKDIKAILNISQAQAQLPFSVFYFIFPATMIISGKILKKLGPQISTIVGGTLFG 79 Query: 89 IGFILSGFIQSKYQLYIT-YGVIAGFGGGMIYLPPIATAPKWWPDRRALATGFAVVGLGL 147 G+I+S F S + I G+IAG G G+ Y+ PI+T KW+PD++ L TG AV G G Sbjct: 80 AGWIISSFGGSNFIFTILGNGLIAGLGAGIAYIVPISTCIKWFPDKKGLITGIAVAGFGG 139 Query: 148 GSFLMGPLATYIIEKPGMGWR--YVFWYCGVAMGIMALIAGAFLEPPPAGWKPAGYTPPA 205 G+ L+ L +I GW VF G I+ ++AG F++ PP+ Y P Sbjct: 140 GAALVSFLGGTLIAN---GWTPFQVFRALGSIFLILIILAGFFMKNPPSNNTHDTYLP-- 194 Query: 206 PPAGAAAPKVTRDWTYEEAKGDTKFWLLYLAYFCGSFAGLMVIGHLAGFGRDAGLTAMAA 265 Y E D KF LY A F G AG V ++ R A +T A Sbjct: 195 -------------LKYRELLVDKKFLFLYFAMFVGLAAGFAVNANIKELSRTASMT--AG 239 Query: 266 AGAVSSLAFSNAATRILSGWFVDK------IGIRVYFAALFALQTAAMIAIFQLGGSVVG 319 AV+ A NA R+ G D+ + + + F A+ + M+ S G Sbjct: 240 VSAVAFFAIFNALGRVSWGALFDRFDYIKSLQLNLLFQAIILFLSPIML------NSATG 293 Query: 320 LSIVAIVIGWNYGAMFTLFPATCLQFYGPTAQGSNYGLLFTACGLAGFAGPWVGGWLKDT 379 L I A++ G NYG + ++ + + +G G YGLLF++ + G P G++ D Sbjct: 294 LQIFAVLTGLNYGGVLVMYAGSVAKIWGAENVGMVYGLLFSS-NIPGALAPIFAGYIYDK 352 Query: 380 TGTYYLPFLCAAALCALGTAIV 401 TG++ + A L LG I+ Sbjct: 353 TGSFTIALYTIAILLILGIIIL 374 Lambda K H 0.327 0.142 0.475 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: 509 Number of extensions: 31 Number of successful extensions: 5 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: 412 Length of database: 380 Length adjustment: 31 Effective length of query: 381 Effective length of database: 349 Effective search space: 132969 Effective search space used: 132969 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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