Align D-lactate transporter, permease component 1 (characterized)
to candidate 3607447 Dshi_0860 inner-membrane translocator (RefSeq)
Query= reanno::Phaeo:GFF1249 (400 letters) >FitnessBrowser__Dino:3607447 Length = 324 Score = 130 bits (327), Expect = 5e-35 Identities = 104/351 (29%), Positives = 148/351 (42%), Gaps = 76/351 (21%) Query: 45 LMQRFVIFGIFAIGFNILFGLTGYLSFGHAAFLGVGSYSAVWM--------------FKL 90 L R I + +G N+ GL G +S GHA F G+G Y+ + F + Sbjct: 33 LATRVAILALAGVGLNLALGLGGMVSLGHALFFGIGGYAMGILAHHAQTFDPLMEAPFVI 92 Query: 91 LSMNVVPAIVLSVI-VAGLFALVIGYVSLRRSGIYFSILTLAFAQMSFNLAYSVLTPITN 149 +P I L+ + ++ L AL +G +SLR +G+YF ++TLAF QM + A S P Sbjct: 93 EGTKSMPVIWLTAMALSALAALAVGALSLRTTGVYFIMITLAFGQMFYYFAIS--WPAYG 150 Query: 150 GETGLQLTLDDPRVLGVSATADGSIPVTSLFGLEMRSTFEMVVGPWAFQFNAGYYLCALI 209 GE GL + + + G +T + + QF + LC + Sbjct: 151 GEDGLSIYVRN--------------------GFPGLNTLDPI------QF---FLLCYGL 181 Query: 210 LLAAFYLSIRIFRSPFGLMLKAVKSNQQRMNYTGLNTRPYTLAAFVISGMYAGLAGGLMA 269 LL A ++ RI SPFGL L + R G + L AF ISG GLAG L A Sbjct: 182 LLLALFVCARITASPFGLALSTARQAPARAETLGFSPFRLRLIAFTISGAITGLAGALFA 241 Query: 270 SMDPLAGAERMQWTASGEVVLMTILGGAGTLIGPVLGAGFIKYFENIFSKINDNVLHSWF 329 ++ W SGE+++ ILGG L GPV GA E+ +++ Sbjct: 242 DLNRFVSPAMFSWHTSGEIMVFVILGGVARLFGPVAGAALFILLEHWLGGLSEY------ 295 Query: 330 SFMPDGIEDAMVFIVHPFIGKGWHLTLGILFMLVVIFLPGGLVEGGQKLRG 380 W + LG L + VV+F GGLV G LRG Sbjct: 296 ----------------------WLIYLGALLLGVVLFAKGGLV--GTLLRG 322 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: 420 Number of extensions: 32 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: 400 Length of database: 324 Length adjustment: 29 Effective length of query: 371 Effective length of database: 295 Effective search space: 109445 Effective search space used: 109445 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: 49 (23.5 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