Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate HSERO_RS22270 HSERO_RS22270 MFS transporter
Query= reanno::WCS417:GFF1429 (438 letters) >FitnessBrowser__HerbieS:HSERO_RS22270 Length = 445 Score = 299 bits (766), Expect = 1e-85 Identities = 167/417 (40%), Positives = 246/417 (58%), Gaps = 3/417 (0%) Query: 6 SARTPQALNKLMFVKLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFF 65 +A + A K + +L+P +++ Y++S+LDR N+ A ++ DLG++ + +GLGAGLFF Sbjct: 16 AAVSEDATMKKVMRRLIPFILLCYVVSYLDRINVGFAALTMNKDLGLTPSQFGLGAGLFF 75 Query: 66 LTYALSEIPSNLIMHKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGL 125 + Y EIPSNL +H+ GAR WI+RIM++WGLIS A AFV G SF + R LLG+AEAG Sbjct: 76 IGYFFFEIPSNLALHRFGARMWISRIMISWGLISMATAFVVGPKSFALARFLLGMAEAGF 135 Query: 126 FPGVMLYLTYWFNREQRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFML 185 PG+ LY T WF R +AT +FL+G+ ANIIG P+ ALM + GM G+ GWQ + +L Sbjct: 136 TPGIYLYFTQWFPGAWRGKATAFFLIGIPVANIIGSPLSGALMELHGMWGFKGWQVLLLL 195 Query: 186 EGLPAVAFAWVVWRKLPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWLTPQ 245 E LPAV + LPDRP+KA WLSA+E + +E ++ E A G+ LK+ T Sbjct: 196 EALPAVLLGVMCLFLLPDRPAKAKWLSADEKQWLENELSTEQNVLAARHGNKLKDAFTNW 255 Query: 246 ILLAIF-VYFCHQITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFA 304 + A+ FC I ++ +LP II ++G L + VGL+ ++P++ A+ L R A Sbjct: 256 RVFALAGANFCGIIGSLSIGLWLPQIIREFG-LPSHQVGLVAAIPYLVGAVAMTLWARLA 314 Query: 305 TTPGRCRRLLVTGLLTMALGLGI-ASVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLK 363 R + ++ AL LGI A + P+ +L ++ Q+ + P+ L Sbjct: 315 NRSERRLFFVAGAIVLAALSLGISAFLHTPLLKMLAITVAVASILSFQATFWAIPSGFLT 374 Query: 364 GVALAGGLGFVNACGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRL 420 G A AGGL + + G LGGFVGPSV+G I ++T L +A L++ A+ L L Sbjct: 375 GRAAAGGLALIVSIGNLGGFVGPSVIGFIREATQGFTYPLIFVAGALLLGAVITLAL 431 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: 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: 445 Length adjustment: 32 Effective length of query: 406 Effective length of database: 413 Effective search space: 167678 Effective search space used: 167678 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