Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate BPHYT_RS28245 BPHYT_RS28245 MFS transporter
Query= reanno::WCS417:GFF1429 (438 letters) >FitnessBrowser__BFirm:BPHYT_RS28245 Length = 442 Score = 324 bits (830), Expect = 4e-93 Identities = 167/409 (40%), Positives = 243/409 (59%), Gaps = 5/409 (1%) Query: 11 QALNKLMFVKLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYAL 70 +A+N + +L+P L++ Y+L+FLDR NI A+ L D G+S AA+ GAG+FF+ YAL Sbjct: 10 EAINSKVMRRLLPFLLLMYVLAFLDRANIGFAQKALQHDTGLSNAAFAFGAGVFFIGYAL 69 Query: 71 SEIPSNLIMHKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVM 130 E+PSNL++H+VGAR W+ RIMVTWGL+SAAM T+FY LR LLG+AEAG FPGV+ Sbjct: 70 FEVPSNLLLHRVGARVWMCRIMVTWGLVSAAMCLAHTPTAFYTLRFLLGVAEAGFFPGVI 129 Query: 131 LYLTYWFNREQRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFMLEG-LP 189 YLT+WF + RARA G F G A I G P+ +L+ + G LG GWQW+F++EG L Sbjct: 130 YYLTHWFPQSARARAVGVFYFGAPLAFIFGSPLSGSLLELHGALGLTGWQWLFLVEGALA 189 Query: 190 AVAFAWVVWRKLPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWLTP-QILL 248 + W W L +RP A WL +E + + ++ + G H + L ++LL Sbjct: 190 SAVGVWAFW-YLDNRPEDARWLEPQERASLRAALDEDALLASAHGPHRILAALVDRRVLL 248 Query: 249 AIFVYFCHQITIYTVIFFLPSIISKY-GELSTMSVGLLTSLPWIAAALGALLIPRFATTP 307 +Y Q+++Y VIF+LP ++ + G + VGL+ +LPW+ A +PR A Sbjct: 249 LSAIYLLIQMSVYGVIFYLPQQVAAFLGTTVGLRVGLVAALPWLCALAVTWYVPRRADRT 308 Query: 308 GRCRRLLVTGLLTMALGLGIAS-VSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVA 366 G RR V L+ LG+G++ V P+F LL C +A F Q + + +P L G A Sbjct: 309 GEHRRWAVVLLIVAGLGIGVSGLVHSPLFGLLALCCAASGFIAAQPLFWTFPTRYLTGAA 368 Query: 367 LAGGLGFVNACGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAAL 415 AGG+ +N+ G LGGF+ PS+ E + + GL V+ + ++AAL Sbjct: 369 AAGGIALINSLGGLGGFIAPSLRTAAEHAFASTSAGLVVLGVSSLLAAL 417 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: 581 Number of extensions: 33 Number of successful extensions: 4 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: 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