Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate BPHYT_RS31140 BPHYT_RS31140 MFS transporter
Query= reanno::WCS417:GFF1429 (438 letters) >FitnessBrowser__BFirm:BPHYT_RS31140 Length = 442 Score = 329 bits (843), Expect = 1e-94 Identities = 171/415 (41%), Positives = 239/415 (57%), Gaps = 6/415 (1%) Query: 21 LMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLIMH 80 ++PL ++ ++++++DR NI + HL DLGI AAAYGLGAGLFF++YA+ E+PSN+++ Sbjct: 28 VLPLFVVMFVVNYIDRVNIGFVRQHLSADLGIGAAAYGLGAGLFFVSYAIFEVPSNMLLQ 87 Query: 81 KVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFNRE 140 + GA+ W+ RIM TWGL + MAFV+GETSFY +RLLLG AEAG FPGV+ Y T W R Sbjct: 88 RFGAKAWLTRIMFTWGLAAVGMAFVRGETSFYAMRLLLGAAEAGFFPGVIFYFTQWLPRG 147 Query: 141 QRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFMLEGLPAVAFAWVVWRK 200 +R +A FL G A+I+ GP+ ALM + G G HGWQWMF++EG+ +V A +W Sbjct: 148 ERGKAMAIFLSGSALASILSGPISGALMLISGG-GLHGWQWMFVIEGMASVVLAGFIWFW 206 Query: 201 LPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWL---TPQILLAIFVYFCHQ 257 L +P A WLS+ E I I +E E W PQIL+ +YF Sbjct: 207 LDSKPRDARWLSSAEQNAIVAEIEEEQRERDAAHAVMPSVWTLLRDPQILIFCVIYFSVS 266 Query: 258 ITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGRCRRLLVTG 317 +TIY F+LPSII K G + VGL S+PW+ + + L A + + Sbjct: 267 LTIYGATFWLPSIIRKMGHFNDFQVGLFNSIPWLISIVAMYLFAMLAARFKFQQAWVACV 326 Query: 318 LLTMALGLGIASVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLGFVNAC 377 LL ALG+ A P+FS + C +A+ F ++ + P L A L +N+ Sbjct: 327 LLIAALGMYAAGQGSPLFSFVAICFAAIGFKAASALFWPIPQGYLDARISAAVLALINSI 386 Query: 378 GLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRLRMGHEPERGAQA 432 G LGGFV P+ G++EQ TG+ GL +A++ VVAA RM +P G A Sbjct: 387 GNLGGFVAPAAFGLLEQKTGSIEGGLTGLAVMSVVAAGVVFFSRM--KPREGRSA 439 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: 556 Number of extensions: 27 Number of successful extensions: 4 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: 438 Length of database: 442 Length adjustment: 32 Effective length of query: 406 Effective length of database: 410 Effective search space: 166460 Effective search space used: 166460 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 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