Align D-lactate transporter, permease component 1 (characterized)
to candidate BPHYT_RS19470 BPHYT_RS19470 ABC transporter permease
Query= reanno::Phaeo:GFF1249 (400 letters) >FitnessBrowser__BFirm:BPHYT_RS19470 Length = 323 Score = 160 bits (404), Expect = 6e-44 Identities = 106/336 (31%), Positives = 159/336 (47%), Gaps = 52/336 (15%) Query: 42 YPDLMQRFVIFGIFAIGFNILFGLTGYLSFGHAAFLGVGSYSAVWMFKLLSMNVVPAIVL 101 YP + + + F +FA FN+L G TG LSFGHA FL Y + + L + ++ Sbjct: 23 YPLFVMKVLCFALFAAAFNLLIGYTGLLSFGHAMFLASAGYVTGYAIQSLGFSPELGVLA 82 Query: 102 SVIVAGLFALVIGYVSLRRSGIYFSILTLAFAQMSFNLAYSVLTPITNGETGLQLTLDDP 161 A L L++G ++RR GIYF+++TLA AQM + + P T+GE GLQ Sbjct: 83 GTAAATLLGLIVGIFAIRRQGIYFAMVTLALAQMVYFVFLQA--PFTHGEDGLQ------ 134 Query: 162 RVLGVSATADGSIPVTSLFG-LEMRSTFEMVVGPWAFQFNAGYYLCALILLAAFYLSIRI 220 +P LFG L++ S + Y++ +++ AF L +RI Sbjct: 135 -----------GVPRGKLFGVLDLSSDVAL------------YFVVLAVMVLAFLLIVRI 171 Query: 221 FRSPFGLMLKAVKSNQQRMNYTGLNTRPYTLAAFVISGMYAGLAGGLMASMDPLAGAERM 280 SPFG +L A+K N+ R G +T + L AF++S AGLAG L + Sbjct: 172 VHSPFGQVLVAIKENEPRAVSLGYDTDRFKLLAFILSAGIAGLAGSLKVLVQGFETLSDA 231 Query: 281 QWTASGEVVLMTILGGAGTLIGPVLGAGFIKYFENIFSKINDNVLHS----WFSFMPDGI 336 WT SG V+LMT++GG GTL GP+LGA I E+ I + + WF Sbjct: 232 YWTMSGLVILMTLVGGMGTLFGPLLGAALIVALEDRLGDIGGALATTTGVEWFR------ 285 Query: 337 EDAMVFIVHPFIGKGWHLTLGILFMLVVIFLPGGLV 372 +G+ + G++F+ V+ G+V Sbjct: 286 ----------SLGESVTIVTGVIFIACVLAFRRGIV 311 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: 425 Number of extensions: 34 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: 323 Length adjustment: 29 Effective length of query: 371 Effective length of database: 294 Effective search space: 109074 Effective search space used: 109074 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