Align D-lactate transporter, permease component 1 (characterized)
to candidate H281DRAFT_06396 H281DRAFT_06396 amino acid/amide ABC transporter membrane protein 2, HAAT family (TC 3.A.1.4.-)
Query= reanno::Phaeo:GFF1249 (400 letters) >FitnessBrowser__Burk376:H281DRAFT_06396 Length = 354 Score = 156 bits (395), Expect = 8e-43 Identities = 111/336 (33%), Positives = 167/336 (49%), Gaps = 57/336 (16%) Query: 45 LMQRFVIFGIFAIGFNILFGLTGYLSFGHAAFLGVGSYSAVWMFKLLSMNVVPAIVLSVI 104 L ++F + A+G N+L G TG LSFG F G+GSYSA + ++ V A++ ++ Sbjct: 50 LATEVLVFALAALGCNLLLGHTGLLSFGQGIFFGLGSYSAGLVLTRAALPVPVALLAAIA 109 Query: 105 VAGLFALVIGYVSLRRSGIYFSILTLAFAQMSFNLAYSVLTP-ITNGETGLQLTLDDPR- 162 V + A ++G+ S+R+ G YF +LTLAF Q+ + LAY+ TP +T G+ GL LD PR Sbjct: 110 VGAIAAALVGWFSIRQRGTYFVMLTLAFGQLFYFLAYT--TPDLTGGDNGL---LDIPRP 164 Query: 163 VLGVSATADGSIPVTSLFGLEMRSTFEMVVGPWAFQFNAGYYLCALILLAAFYLSIRIFR 222 LG+ A IP+ S PW + Y A++ L F+L +R+ Sbjct: 165 ALGLPGKA--LIPLAS---------------PWQY-----YGFVAVLFLVVFWLLMRVSH 202 Query: 223 SPFGLMLKAVKSNQQRMNYTGLNTRPYTLAAFVISGMYAGLAGGLMASMDPLAGAERMQW 282 S FG L A++ N+ R G + + + L AFVISG GLAG L A M +A + + Sbjct: 203 SVFGRTLLAIRDNEARAAAVGYDVKRFKLMAFVISGAVTGLAGALHALMTGIAPLSNIDY 262 Query: 283 TASGEVVLMTILGGAGTLIGPVLGAGFIKYFENIFSKINDNVLHSWFSFMPDGIEDAMVF 342 S +++MT++GG G L VLGA F F + W S Sbjct: 263 HTSEMILVMTVIGGTGNLFASVLGAAFYVLFAD------------WLS------------ 298 Query: 343 IVHPFIGKGWHLTLGILFMLVVIFLPGGLVEGGQKL 378 + W L LGI+ M V +++ GL G+++ Sbjct: 299 ----TLWPRWLLLLGIVLMAVSLYMQRGLWGLGERI 330 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: 404 Number of extensions: 32 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: 354 Length adjustment: 30 Effective length of query: 370 Effective length of database: 324 Effective search space: 119880 Effective search space used: 119880 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