Align L-lactate permease (characterized)
to candidate 8499614 DvMF_0381 L-lactate transport (RefSeq)
Query= SwissProt::P33231 (551 letters) >FitnessBrowser__Miya:8499614 Length = 506 Score = 294 bits (753), Expect = 5e-84 Identities = 184/526 (34%), Positives = 287/526 (54%), Gaps = 38/526 (7%) Query: 15 WLSSLIASLPILFFFFALIKLKLKGYVAASWTVAIALAVALL-FYKMPVANALASVVYGF 73 +L A PI++ F+L+ LKL Y + T+ LA+A+ ++KMP AL++ + G Sbjct: 6 YLQLAAALAPIVWLIFSLVVLKLPAYRTCALTLVCTLALAVFGWWKMPAFMALSAALEGA 65 Query: 74 FYGLWPIAWIIIAAVFVYKISVKTGQFDIIRSSILSITPDQRLQMLIVGFCFGAFLEGAA 133 LWPI +IIAAVF Y ++ TG D+I + SIT D+RL +LIV + FG FLEG A Sbjct: 66 AMALWPIMIVIIAAVFTYNLARHTGSMDVITRMLSSITTDKRLLVLIVAWGFGGFLEGVA 125 Query: 134 GFGAPVAITAALLVGLGFKPLYAAGLCLIVNTAPVAFGAMGIPILVAGQVTGIDSFEIGQ 193 G+G VAI A++L +GF+P++AA +CL+ NT P AFGA+GIPI+ VTG+ I Sbjct: 126 GYGTAVAIPASILAAMGFQPMFAAVICLVANTVPTAFGAIGIPIVTMAGVTGLPVETISY 185 Query: 194 MVGRQLPFMTIIVLFWIMAIMDGWRGIKETWPAVVVAGGSFAIAQYLSSNFIGPELPDII 253 QL I++ + ++ + G++GIK + A +V+G +FA Q ++ ++G ELP +I Sbjct: 186 YTALQLFVFIILITYLLVILTAGFKGIKGVFWATLVSGLAFAFPQLYTAKYMGAELPCLI 245 Query: 254 SSLVSLLCLTLFLKRWQPVRVFRFGDLGASQVDMTLAHTGYTAGQVLRAWTPFLFLTATV 313 S+ S++ ++ R+F A+QVD A + ++AW P++ + A + Sbjct: 246 GSVCSMIATIVW------ARLFHRDT--AAQVD------PIPAAEKVKAWLPYILVFAFI 291 Query: 314 TLWSIPPFKALFASGGALYEWVINIPVPYLDKLVARMPPVVSEATAYAAVFKFDWFSATG 373 L S F A+ + G++ V ++ P F F W + G Sbjct: 292 ILCS-NLFPAIRDALGSVKTTV---------RIYGDNP------------FTFKWIATPG 329 Query: 374 TAILFAALLSIVWLKMKPSDAISTFGSTLKELALPIYSIGMVLAFAFISNYSGLSSTLAL 433 I+ A + + +K + GST K+L ++ ++A A + + SG+ +T+A+ Sbjct: 330 ALIIIATYIGGMIQGVKVREITGVLGSTAKKLVYSGVTVVSIVALAKVMSTSGMINTIAI 389 Query: 434 ALA-HTGHAFTFFSPFLGWLGVFLTGSDTSSNALFAALQATAAQQIGVSDLLLVAANTTG 492 A+A T F F SP LG LG F+TGSDTSSN LF LQ A +I + +V+A+ G Sbjct: 390 AVADSTSSYFPFISPLLGALGTFVTGSDTSSNVLFGQLQMEVANRISIDSTWIVSASAAG 449 Query: 493 GVTGKMISPQSIAIACAAVGLVGKESDLFRFTVKHSLIFTCIVGVI 538 GKMISPQSIA+A AA GL G E + T+ + + ++G + Sbjct: 450 ATAGKMISPQSIAVATAATGLTGYEGRIMNRTLAVCVGYVLVLGTL 495 Lambda K H 0.328 0.140 0.436 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: 735 Number of extensions: 32 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 551 Length of database: 506 Length adjustment: 35 Effective length of query: 516 Effective length of database: 471 Effective search space: 243036 Effective search space used: 243036 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: 52 (24.6 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