Align L-lactate permease (characterized, see rationale)
to candidate PP_4735 PP_4735 L-lactate permease
Query= uniprot:Q8EIL2 (545 letters) >FitnessBrowser__Putida:PP_4735 Length = 556 Score = 767 bits (1980), Expect = 0.0 Identities = 381/552 (69%), Positives = 462/552 (83%), Gaps = 12/552 (2%) Query: 2 TWTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMPV 61 TW Q Y+PLGSL L+A+ A++PIVFFFLAL V +LKGH+AG++TL +++ VAI ++MPV Sbjct: 3 TWQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALSILVAIFAFQMPV 62 Query: 62 SIALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLVG 121 +ALA+A YGF YGLWPIAWII+ AVFLYK+TVK+GQFE+IRSSV+S+T+DQRLQ+LL+G Sbjct: 63 DMALAAAGYGFLYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLLIG 122 Query: 122 FSFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQ 181 F FGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGA+GIPIIVAGQ Sbjct: 123 FCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVAGQ 182 Query: 182 VSSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLTS 241 V+ +D FHIG + GRQLP+LS+ VPFWL+ MMDG+RG+++TWPA LVAG+SFAVTQ+ TS Sbjct: 183 VTGIDAFHIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVKETWPAALVAGLSFAVTQYFTS 242 Query: 242 NFIGPELPDITSALVSLICLTLFLKVWQPKEIFT------FSGMKQRAVTPKSTFSNGQI 295 NFIGPELPDITSAL SLICLTLFLKVWQPK F+ + + Q + + S +S G+I Sbjct: 243 NFIGPELPDITSALASLICLTLFLKVWQPKRAFSEAKGSVGAAVVQPSGSQPSPYSFGEI 302 Query: 296 FKAWSPFIILTAIVTLWSIKDVQLALSFA------TISIEVPYLHNLVIKTAPIVAKETP 349 FKAWSPF+ILT +VT+W++K + A + + +P+L LVIKTAPIVA T Sbjct: 303 FKAWSPFLILTVLVTIWTLKPFKAAFAPGGAMYNFVFNFAIPHLDQLVIKTAPIVAAPTA 362 Query: 350 YAAIYKLNLLGAVGTAILIAAMISIVVLKMSISNALTSFKDTLIELRFPILSIGLVLAFA 409 A++KL+ + A GTAI ++A+IS+ VLK++ LT+FK+T ELR+PILSIG+VLAFA Sbjct: 363 MPAVFKLDPISATGTAIFLSALISMAVLKINFKTGLTTFKETFWELRWPILSIGMVLAFA 422 Query: 410 FVANYSGLSSTLALVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGALQANTANQIG 469 FV NYSG+SST+ALVLAGTG AFPFFSPFLGWLGVFLTGSDTSSNALF +LQA TA+QIG Sbjct: 423 FVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNALFSSLQATTAHQIG 482 Query: 470 VTPELLVAANTTGGVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLFFCTFIGVLT 529 V LLVAANT+GGVTGKMISPQSIAVACAATGL GKESDLFRFT+KHSLFF T +G++T Sbjct: 483 VNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTVKHSLFFATIVGLIT 542 Query: 530 VLQAYIVPWTLV 541 ++QAY + LV Sbjct: 543 LVQAYWLTGMLV 554 Lambda K H 0.327 0.140 0.419 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: 1108 Number of extensions: 42 Number of successful extensions: 3 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: 545 Length of database: 556 Length adjustment: 36 Effective length of query: 509 Effective length of database: 520 Effective search space: 264680 Effective search space used: 264680 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