Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate WP_011654781.1 RL_RS29855 MFS transporter
Query= reanno::WCS417:GFF1429 (438 letters) >NCBI__GCF_000009265.1:WP_011654781.1 Length = 430 Score = 285 bits (730), Expect = 1e-81 Identities = 143/397 (36%), Positives = 229/397 (57%), Gaps = 2/397 (0%) Query: 20 KLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLIM 79 KLMP L I Y+++++DR N++ AK + LG+S AYGLGA LFF+ Y L E+PSNL + Sbjct: 14 KLMPFLGILYLIAYIDRQNVSFAKLQMVDALGMSEYAYGLGASLFFIGYFLFEVPSNLFL 73 Query: 80 HKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFNR 139 ++GAR W ARI+V+WG+++ A+AF Q T FY+LR LLG+ EAG FPGV+ LT WF Sbjct: 74 DRLGARVWFARILVSWGIVTIALAFTQNATMFYILRFLLGVCEAGFFPGVLYLLTLWFPS 133 Query: 140 EQRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFMLEGLPAVAFAWVVWR 199 R R G F++ AN +G P+G L+ +DG+ G+ GW+W+F+ G+PAV V + Sbjct: 134 TYRGRMVGLFMIFSAIANAVGAPLGGVLLDLDGLYGFAGWEWVFLATGVPAVIAGIVTFF 193 Query: 200 KLPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWLTPQILLAIFVYFCHQIT 259 LP RP A +L+ +E + +E+R+ E G+ K + P++LL Y ++ Sbjct: 194 YLPGRPENASFLNDDEKQWLERRLTSENAGMGEHAGNGFKALIDPRVLLMALCYIAFPLS 253 Query: 260 IYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFA-TTPGRCRRLLVTGL 318 Y + ++LP+I+ +G +T++ G L +PW+ A+ ++P A + +++ Sbjct: 254 AYGLSYWLPTIVKAFGVSNTVN-GFLNIIPWVLVAIALYVVPAMADKAQSKTPYIVIPAF 312 Query: 319 LTMALGLGIASVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLGFVNACG 378 + A L A + C++A F Q + + P+ LKG A GL +N+ G Sbjct: 313 IGAACLLLSALIPNHTLQFAFLCVAAAGIFAPQPVFWSLPSRFLKGAGAAAGLAAINSVG 372 Query: 379 LLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAAL 415 LGGFV +V+ I++++G+ + + +A L AL Sbjct: 373 NLGGFVAQNVVPWIKEASGSTIAPMFFLAACLAAGAL 409 Lambda K H 0.327 0.141 0.438 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: 584 Number of extensions: 34 Number of successful extensions: 5 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: 438 Length of database: 430 Length adjustment: 32 Effective length of query: 406 Effective length of database: 398 Effective search space: 161588 Effective search space used: 161588 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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