Align 2-Deoxy-D-ribose porter, DeoP (characterized)
to candidate CA265_RS04675 CA265_RS04675 L-fucose:H+ symporter permease
Query= TCDB::Q8XEV7 (438 letters) >FitnessBrowser__Pedo557:CA265_RS04675 Length = 436 Score = 241 bits (614), Expect = 4e-68 Identities = 134/406 (33%), Positives = 218/406 (53%), Gaps = 6/406 (1%) Query: 19 LFQFILLSCLFPLWGCAAALNDILITQFKSVFSLSNFASALVQSAFYGGYFLIAIPASLV 78 LF IL++ LF WG L+ +LI + F L+ F S LV S+ + YFL+A+PA + Sbjct: 22 LFPLILVTSLFFFWGFVHNLDPVLIPHLRKAFQLNVFESTLVDSSVFIAYFLLALPAGYI 81 Query: 79 IKKTSYKVAILIGLTLYIVGCTLFFPASHMATYTMFLAAIFAIAIGLSFLETAANTYSSM 138 ++K YK I++GL L+ +GC LF PA++ A Y FL A+F IA GL+FLETAAN Y ++ Sbjct: 82 MRKYGYKSGIILGLVLFAIGCLLFIPAANTAQYIFFLGALFIIACGLTFLETAANPYVTV 141 Query: 139 IGPKAYATLRLNISQTFYPIGAAAGILLGKYLVFSEGESLEKQMAGMNAEQVHNFKVLML 198 +GP AT RLN SQ+F + A +LG +F+E + + Q+A M + + + Sbjct: 142 LGPPETATQRLNFSQSFNGLAAFLAPVLGGKFIFTEVKYTDAQLAKMLPLEKQAYMLEEA 201 Query: 199 ENTLEPYKYMIMVLVVVMVLFLLTRFPTCKVAQTASHKRPSALDTLRYLASNARFRRGIV 258 PY + ++++VV +LF+ T+ P K + A K + ++ ++ R I+ Sbjct: 202 STVKAPYLILGILIIVVAILFIFTKLPDIKEEENAQEK-----SSFSHVLGHSHLRWAII 256 Query: 259 AQFLYVGMQVAVWSFTIRLALELGDINERDASTFMVYSFACFFIGKFIANILMTRFNPEK 318 QF YVG QV V S I I++ A + + F +G+F M K Sbjct: 257 GQFFYVGAQVCVLSLFISFVTSSAGISQDAAKWYAGAAGLAFMVGRFAGTFFMRYVAAHK 316 Query: 319 VLILYSVIGALFLAYVALAPSFSAVYVAVLVSVLFGPCWATIYAGTLDTVDNEHTEMAGA 378 +L+LY++I A+ A VY + VS + TI++ + + + T++ + Sbjct: 317 LLMLYALISAVLTLVSIFASGMITVYALIGVSFFMSIMFPTIFSLGIAGLGKD-TKLGSS 375 Query: 379 VIVMAIVGAAVVPAIQGYVADMFHSLQLSFLVSMLCFVYVGVYFWR 424 +IVM+IVG A +P + G ++D H++Q +LV +CF+ V + W+ Sbjct: 376 LIVMSIVGGAFLPPVLGLISDATHNIQYGYLVPFVCFLVVFYFGWK 421 Lambda K H 0.329 0.139 0.412 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: 484 Number of extensions: 28 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: 436 Length adjustment: 32 Effective length of query: 406 Effective length of database: 404 Effective search space: 164024 Effective search space used: 164024 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 (21.8 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