Align D-lactate transporter, permease component 1 (characterized)
to candidate BPHYT_RS32505 BPHYT_RS32505 ABC transporter permease
Query= reanno::Phaeo:GFF1249 (400 letters) >FitnessBrowser__BFirm:BPHYT_RS32505 Length = 351 Score = 155 bits (391), Expect = 2e-42 Identities = 110/356 (30%), Positives = 168/356 (47%), Gaps = 55/356 (15%) Query: 45 LMQRFVIFGIFAIGFNILFGLTGYLSFGHAAFLGVGSYSAVWMFKLLSMNVVPAIVLSVI 104 L ++F + A+G N+L G TG LSFG F G+GSY A + + V A++ S + Sbjct: 50 LATEVLVFALAALGCNLLLGHTGLLSFGQGIFFGLGSYCAGLVLTKTGLPVSMALLASAV 109 Query: 105 VAGLFALVIGYVSLRRSGIYFSILTLAFAQMSFNLAYSVLTP-ITNGETGLQLTLDDPRV 163 + A ++G+ S+R+ G YF +LTLAF Q+ + LAY+ TP +T G+ GL LD PR Sbjct: 110 IGAAAAALVGWFSIRQRGTYFVMLTLAFGQLFYFLAYT--TPDLTGGDNGL---LDIPR- 163 Query: 164 LGVSATADGSIPVTSLFGLEMRSTFEMVVGPWAFQFNAGYYLCALILLAAFYLSIRIFRS 223 P LFG + PW + Y A++ L F+L +R+ S Sbjct: 164 -----------PALGLFG----KALVPLTSPWQY-----YGFVAVLFLVVFWLLMRVSHS 203 Query: 224 PFGLMLKAVKSNQQRMNYTGLNTRPYTLAAFVISGMYAGLAGGLMASMDPLAGAERMQWT 283 FG L A++ N+ R G + + + L AFVISG GLAG L A M +A + + Sbjct: 204 VFGRTLLAIRDNEARAAAVGYDVKRFKLMAFVISGAVTGLAGALHALMTGIAPLSNIDYH 263 Query: 284 ASGEVVLMTILGGAGTLIGPVLGAGFIKYFENIFSKINDNVLHSWFSFMPDGIEDAMVFI 343 S +++MT++GG G L VLGA F F + W S Sbjct: 264 TSEMILVMTVIGGTGNLFASVLGAAFYVLFAD------------WLS------------- 298 Query: 344 VHPFIGKGWHLTLGILFMLVVIFLPGGLVEGGQKLRGWIQGRKAKKDGPSGKTEPA 399 + W L LGI+ + V +++ GL G+++ ++ + + G E A Sbjct: 299 ---TLWPRWLLLLGIVLIAVSLYMQRGLWGLGERVWQSLRRKSSADAGNDADKESA 351 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: 38 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 400 Length of database: 351 Length adjustment: 30 Effective length of query: 370 Effective length of database: 321 Effective search space: 118770 Effective search space used: 118770 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