Align D-lactate transporter, permease component 1 (characterized)
to candidate 3607994 Dshi_1402 inner-membrane translocator (RefSeq)
Query= reanno::Phaeo:GFF1249 (400 letters) >FitnessBrowser__Dino:3607994 Length = 402 Score = 605 bits (1559), Expect = e-178 Identities = 298/403 (73%), Positives = 354/403 (87%), Gaps = 4/403 (0%) Query: 1 MFTLNKKDKTLLLVVAILTLFAPFILNPFPTGSALAQFNAGYPDLMQRFVIFGIFAIGFN 60 MF L KKD LLL+VA LT+ APF+LNPFP GS +AQFNAGYPDLMQRFVIFGIFAIGFN Sbjct: 1 MFGLEKKDTVLLLIVAGLTMLAPFLLNPFPEGSGMAQFNAGYPDLMQRFVIFGIFAIGFN 60 Query: 61 ILFGLTGYLSFGHAAFLGVGSYSAVWMFKLLSMNVVPAIVLSVIVAGLFALVIGYVSLRR 120 ILFGLTGYLSFGHAAFLGVGSY+A+WM KLL+MNV+PAI++++++AGLF+L++G++SLRR Sbjct: 61 ILFGLTGYLSFGHAAFLGVGSYAAIWMMKLLTMNVIPAIIMAIVLAGLFSLLVGWISLRR 120 Query: 121 SGIYFSILTLAFAQMSFNLAYSVLTPITNGETGLQLTLDDPRVLGVSATADGSIPVTSLF 180 SGIYFSILTLAFAQMS+ LAYSVLTPIT GETGLQ ++DPR+L A A+G+ P +LF Sbjct: 121 SGIYFSILTLAFAQMSYALAYSVLTPITGGETGLQPKVNDPRLLD-PALAEGATPSANLF 179 Query: 181 GLEMRSTFEMVVGPWAFQFNAGYYLCALILLAAFYLSIRIFRSPFGLMLKAVKSNQQRMN 240 GL M+S++E+ VG W F FNAGYYL A+I+L +FY++IRIFRSPFG+ML+AVKSNQQRMN Sbjct: 180 GLTMKSSYELNVGGWLFTFNAGYYLAAVIMLISFYVAIRIFRSPFGMMLRAVKSNQQRMN 239 Query: 241 YTGLNTRPYTLAAFVISGMYAGLAGGLMASMDPLAGAERMQWTASGEVVLMTILGGAGTL 300 YTGLN++PYTLAAFVISGMYAGLAGGLM +MD G ERM WTASGEVVLMTILGGAGTL Sbjct: 240 YTGLNSKPYTLAAFVISGMYAGLAGGLMVAMDTQVGPERMFWTASGEVVLMTILGGAGTL 299 Query: 301 IGPVLGAGFIKYFENIFSKINDNVLHSWFSFMPDGIEDAMVFIVHPFIGKGWHLTLGILF 360 IGPVLGAG IKY ENI SKIN+ +LH WF+F+PDG+EDA+V +V+PFIGKGWHLTLGI+F Sbjct: 300 IGPVLGAGMIKYMENIISKINETILHQWFAFLPDGMEDALVAMVYPFIGKGWHLTLGIIF 359 Query: 361 MLVVIFLPGGLVEGGQKL-RGWIQGRKAKKDG--PSGKTEPAE 400 MLVVIFLPGGLVEGGQ++ R + +G+KA +G S +T PAE Sbjct: 360 MLVVIFLPGGLVEGGQRIARLFGRGKKADAEGDKKSAETTPAE 402 Lambda K H 0.327 0.143 0.435 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: 685 Number of extensions: 29 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: 400 Length of database: 402 Length adjustment: 31 Effective length of query: 369 Effective length of database: 371 Effective search space: 136899 Effective search space used: 136899 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