Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate BWI76_RS19985 BWI76_RS19985 MFS transporter
Query= reanno::WCS417:GFF1429 (438 letters) >FitnessBrowser__Koxy:BWI76_RS19985 Length = 429 Score = 289 bits (740), Expect = 1e-82 Identities = 151/405 (37%), Positives = 231/405 (57%), Gaps = 5/405 (1%) Query: 20 KLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLIM 79 +L+P ++ Y+L+FLDR+NI AK +D G+S AY LGAG+FF+ YA +P+NL+M Sbjct: 16 RLIPFMLALYVLAFLDRSNIGFAKETYQLDTGLSNEAYALGAGIFFVVYAFLGVPANLLM 75 Query: 80 HKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFNR 139 K GAR WI + WGL+SAAMA+ E F ++R LLG AEAG FPG++ + WF + Sbjct: 76 RKFGARKWIGCTTLLWGLLSAAMAWADTEAKFLLVRTLLGAAEAGFFPGMIYLTSQWFPQ 135 Query: 140 EQRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFMLEGLPAVAFAWVVWR 199 + RA G F +G A +G P+ AL+ M G +G GW WMF++EGL AV + + Sbjct: 136 QNRASIMGLFYMGAPLALTLGSPLSGALLEMHGFMGHPGWFWMFIIEGLLAVGAGFFTFF 195 Query: 200 KLPDRPSKAPWLSAEEARGIEQRIA-QETEEGAGEGGHSLKNWLTPQILLAIFVYFCHQI 258 L D P KA +LSA E + + +A +E ++ +L+N Q+ + +Y Q+ Sbjct: 196 WLDDTPQKARFLSAAEKQALISELASEEQKKVTSRLSDALRNGRVWQLAI---IYLTIQV 252 Query: 259 TIYTVIFFLPS-IISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGRCRRLLVTG 317 +Y +IFFLP+ + + G ++T++PW+AA G LIPR++ G R + Sbjct: 253 AVYGLIFFLPTQVAALLGTKVGFVASVVTAIPWVAALFGTWLIPRYSDRTGERRNIAAFT 312 Query: 318 LLTMALGLGIASVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLGFVNAC 377 LL A+G+ ++ + PV +++ C++AV VQ + + P L G ALA G+GFVN Sbjct: 313 LLAAAIGIAVSGLVSPVLAIIALCVAAVGVIAVQPVFWTMPTQLLSGTALAAGIGFVNLF 372 Query: 378 GLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRLRM 422 G +GGF+ P + E + GL +A V +V + LR+ Sbjct: 373 GAIGGFLAPIIRVQAETMFASDSAGLVTLACVAIVGVVIIFSLRV 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: 512 Number of extensions: 31 Number of successful extensions: 3 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: 429 Length adjustment: 32 Effective length of query: 406 Effective length of database: 397 Effective search space: 161182 Effective search space used: 161182 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