Align L-lactate and D-lactate permease (lctP family) (characterized)
to candidate RR42_RS21280 RR42_RS21280 L-lactate permease
Query= reanno::pseudo5_N2C3_1:AO356_07550 (564 letters) >FitnessBrowser__Cup4G11:RR42_RS21280 Length = 580 Score = 822 bits (2124), Expect = 0.0 Identities = 422/580 (72%), Positives = 477/580 (82%), Gaps = 16/580 (2%) Query: 1 MQTWQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALAIAVAIFAFNM 60 MQ W Q Y+PLGSL LSALAA +PI+FFFLALAV R+KGHVA +ITL LA+ VAIFA+ M Sbjct: 1 MQPWTQTYTPLGSLWLSALAAALPILFFFLALAVLRMKGHVAAAITLLLALGVAIFAYGM 60 Query: 61 PADMAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLL 120 P A AAAG+GFAYGLWPIAWIIV AVFLYK+ VK+GQF++IR+SVL+ITDDQRLQ+LL Sbjct: 61 PVPQALAAAGFGFAYGLWPIAWIIVTAVFLYKIVVKTGQFDIIRASVLAITDDQRLQMLL 120 Query: 121 IGFCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVA 180 IGF FGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGA+GIPIIVA Sbjct: 121 IGFAFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVA 180 Query: 181 GQVTGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVRETWPAALVAGLSFAITQYF 240 GQVTGIDA IGAM GRQLPLLSL VPFWLVF+MDG RGV+ETWPAALV G SF++TQYF Sbjct: 181 GQVTGIDAMHIGAMAGRQLPLLSLAVPFWLVFIMDGKRGVKETWPAALVTGASFSVTQYF 240 Query: 241 TSNFIGPELPDITSALASLISLTLFLKVWQPK----RTAGAQIAGATSSATVTASVG--- 293 TSN IGPELPDITSAL SL+SLTLFLKVWQPK R GA AG ++A G Sbjct: 241 TSNHIGPELPDITSALVSLVSLTLFLKVWQPKSASQRAGGAVKAGGGAAALARMGGGLAS 300 Query: 294 ---------GFGQPRSTVASPYSLGEIIKAWSPFLILTVLVTIWTLKPFKAMFAAGGSMY 344 G G + ASPY++ + ++AW+PF ILT +VT+W+L FKA+F G++ Sbjct: 301 DAGSFGNGAGDGAGNNRRASPYTVAQTVRAWAPFGILTAIVTVWSLPSFKALFVGNGALA 360 Query: 345 GWVFNFAIPHLDQMVIKVAPIVINPTAIPAVFKLDPISATGTAIFFSALISMLVLKINIK 404 GWV F +P LDQ+VIK APIV P A AVFKLD +SA GTAI +ALIS ++L++ Sbjct: 361 GWVLKFHVPALDQLVIKAAPIVAQPKAYEAVFKLDLVSAVGTAILLTALISAVLLRMKPG 420 Query: 405 TGLTTFKETLFELRWPILSIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWL 464 L TF ETL ELR PILSIG+VL FAFV NYSGMSST+AL+LAGTGAAFPFFSPFLGWL Sbjct: 421 AALATFGETLMELRRPILSIGLVLGFAFVANYSGMSSTLALLLAGTGAAFPFFSPFLGWL 480 Query: 465 GVFLTGSDTSSNALFSSLQATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATG 524 GVFLTGSDTSSNALF SLQ+TTAHQIGV+DTLLVAANT+GGVTGKMISPQSIAVACAATG Sbjct: 481 GVFLTGSDTSSNALFCSLQSTTAHQIGVSDTLLVAANTTGGVTGKMISPQSIAVACAATG 540 Query: 525 LVGKESDLFRFTLKHSLFFATIVGLITLAQAYWFTGMLVH 564 LVGKES+LFRFT+KHSL FA IVG+IT+ QAY TGM+ H Sbjct: 541 LVGKESELFRFTVKHSLLFAMIVGIITMLQAYVLTGMIPH 580 Lambda K H 0.327 0.139 0.422 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: 961 Number of extensions: 36 Number of successful extensions: 2 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: 564 Length of database: 580 Length adjustment: 36 Effective length of query: 528 Effective length of database: 544 Effective search space: 287232 Effective search space used: 287232 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: 53 (25.0 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