Align L-lactate transporter; SfMCT (characterized)
to candidate 206601 DVU1163 major facilitator superfamily protein
Query= SwissProt::A0LNN5 (412 letters) >MicrobesOnline__882:206601 Length = 424 Score = 171 bits (433), Expect = 4e-47 Identities = 112/363 (30%), Positives = 175/363 (48%), Gaps = 12/363 (3%) Query: 28 LYAWSVFIKPLNAEFGWSRAEIAMAFAICCLIFGLMTFPAGRLSDKMGPRKVVMTGGVLL 87 +YA+SV PLN GW ++ I +AF++ L G GR +KMGPR G+L Sbjct: 24 VYAYSVMTLPLNQLHGWQKSNITLAFSLAILFLGFSAAFLGRSVEKMGPRNSGRLAGILY 83 Query: 88 AIGFILSGF---IQSKYQLYITYGVIAGFGGGMIYLPPIATAPKWWPDRRALATGFAVVG 144 G + +G + S ++YGVI G G G+ Y+ P++T KW+PDRR LATG A++G Sbjct: 84 TAGIMGAGIAVKLGSLPLFLLSYGVIGGIGLGVGYITPVSTLVKWFPDRRGLATGMAIMG 143 Query: 145 LGLGSFLMGPLATYIIEKPGMGWRYVFWYCGVAMGIMALIAGAFLEPPPAGWKPAGYTPP 204 G + + GP+ + + + W+ V++ G + + +L PPP GW P GY Sbjct: 144 FGFAAMIFGPIMAKLFQIMEI-WQ-VYFVLGAIYFCLIYGSSLYLAPPPEGWVPPGYAAQ 201 Query: 205 A-PPAGAAAPKVTRDWTYEEAKGDTKFWLLYLAYFCGSFAGLMVIGHLAGFGRDA-GLTA 262 AG + +T EA +F+ ++L F G+ +I + ++ GL+ Sbjct: 202 GQQSAGRTLKRDLGQYTVAEAIRTKRFYFMWLMLFINITCGIALISVASPMAQEVIGLSP 261 Query: 263 MAAAGAVSSLAFSNAATRILSGW--FVDKIGIRVYFAALFALQTAAMIAIFQLGGSVVGL 320 M AA V + N RI GW D +G + A F +Q A +A+ S +G Sbjct: 262 MQAATMVGLMGLFNGGGRI--GWASLSDYLGRGRTYMAFFLIQICAFMAL-TTTTSHLGF 318 Query: 321 SIVAIVIGWNYGAMFTLFPATCLQFYGPTAQGSNYGLLFTACGLAGFAGPWVGGWLKDTT 380 + +I YG F+ PA +G G+ +G TA G+AG GP + + + T Sbjct: 319 QCLIFIILTCYGGGFSTLPAFLGDMFGTKQLGTIHGYELTAWGIAGMVGPSIVTRVLEAT 378 Query: 381 GTY 383 G+Y Sbjct: 379 GSY 381 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: 622 Number of extensions: 46 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: 412 Length of database: 424 Length adjustment: 32 Effective length of query: 380 Effective length of database: 392 Effective search space: 148960 Effective search space used: 148960 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 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