Align 2-Deoxy-D-ribose porter, DeoP (characterized)
to candidate N515DRAFT_1222 N515DRAFT_1222 MFS transporter, FHS family, L-fucose permease
Query= TCDB::Q8XEV7 (438 letters) >FitnessBrowser__Dyella79:N515DRAFT_1222 Length = 422 Score = 253 bits (647), Expect = 6e-72 Identities = 143/396 (36%), Positives = 221/396 (55%), Gaps = 4/396 (1%) Query: 24 LLSCLFPLWGCAAALNDILITQFKSVFSLSNFASALVQSAFYGGYFLIAIPASLVIKKTS 83 L+ LF LWG A LND+LI QFK F L++F + LVQSAFY GYFL+A+PA + +++ Sbjct: 18 LIVSLFFLWGVANNLNDVLIPQFKKAFVLNDFQAGLVQSAFYLGYFLVAMPAGIYMRRFG 77 Query: 84 YKVAILIGLTLYIVGCTLFFPASHMATYTMFLAAIFAIAIGLSFLETAANTYSSMIGPKA 143 YK A++ GL LY +G LF+PA+ TY FL A+F IA GL+FLET+AN + +++GP+ Sbjct: 78 YKSAVVFGLALYGLGALLFWPAAQQGTYGFFLFALFVIASGLAFLETSANPFVTLLGPRE 137 Query: 144 YATLRLNISQTFYPIGAAAGILLGKYLVFSEGESLEKQMAGMNAEQVHNFKVLMLENTLE 203 A RLN++Q F P+G+ GIL+G++ +FS E +Q+A ++A + F Sbjct: 138 SAARRLNLAQAFNPLGSITGILIGQHFIFSGVEHTPEQLAALSAAERAAFVAHETAAVQL 197 Query: 204 PYKYMIMVLVVVMVLFLLTRFPTCKVAQTASHKRPSALDTLRYLASNARFRRGIVAQFLY 263 PY + +V++ +L LLTRFP + + R L L + RF + AQF Y Sbjct: 198 PYLAIGLVVLAWGLLILLTRFPAVHAVEEGAVPRDHG--ALARLLGDRRFLATLAAQFFY 255 Query: 264 VGMQVAVWSFTIR-LALELGDINERDASTFMVYSFACFFIGKFIANILMTRFNPEKVLIL 322 VG QV VWS+ IR + + + A+ +M+ S ACF G+F + LM P ++L L Sbjct: 256 VGAQVGVWSYLIRYVQATMPGTPAKLAANYMLVSLACFMAGRFAGSALMRYVAPRRLLAL 315 Query: 323 YSVIGALFLAYVALAPSFSAVYVAVLVSVLFGPCWATIYAGTLDTVDNEHTEMAGAVIVM 382 ++ + + P + V S + TI+A ++ ++ ++ A++VM Sbjct: 316 FAAVNVALTVFAVAVPGVAGACALVACSFFMSVMYPTIFALGVEGRGDDERKLGSALLVM 375 Query: 383 AIVGAAVVPAIQGYVADMFHSLQLSFLVSMLCFVYV 418 I+G AV+ A G V+D + + LV FV + Sbjct: 376 TIIGGAVLTAAMGAVSDA-AGISRAMLVPAASFVVI 410 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: 404 Number of extensions: 24 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: 422 Length adjustment: 32 Effective length of query: 406 Effective length of database: 390 Effective search space: 158340 Effective search space used: 158340 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