Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate RR42_RS03360 RR42_RS03360 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Cup4G11:RR42_RS03360 Length = 537 Score = 304 bits (779), Expect = 4e-87 Identities = 190/506 (37%), Positives = 283/506 (55%), Gaps = 20/506 (3%) Query: 6 LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRD-AGSIL 64 LL ++ K + GV ALR L+ AG VHAL G NGAGKST + IL G D G Sbjct: 10 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 69 Query: 65 LNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRT 124 ++G VQ + P A G+A+I QEL P ++VAENI+LGR +R G + + R Sbjct: 70 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMV-RAC 128 Query: 125 RELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFK 184 L L D + + LS+AQ QLVEIA+A + ++++MDEPT+ + HE LF Sbjct: 129 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 188 Query: 185 AIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQEL 244 IR+L +G I+Y+SHR++E+ ++AD ++ RDG FV + A + + LV+ +VG++L Sbjct: 189 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 248 Query: 245 TRIDHKV-GRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIY 303 + K G+ L V +++ S LR GE+LG+ GL+G+GR+E ++ Sbjct: 249 SGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVF 308 Query: 304 GLTVADSGSVTLQGK-------PMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIA 356 G G V + +P G P+ I+AG++ +TEDRK GL L S+ NI Sbjct: 309 GADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENIN 368 Query: 357 LSAYKR----LSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKC 412 L R L + AR+ T A D L I+ ++ V ++SGGNQQKV+L++ Sbjct: 369 LIVAARDALGLGRLNRTAARRRTTEAID---TLGIRVAHAQVNVGALSGGNQQKVMLSRL 425 Query: 413 LSTEPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFK 472 L +P L+ DEPTRG+D GAK EIY L++ + G A +++SSE PE++ L DR+ V + Sbjct: 426 LEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMR 485 Query: 473 GGRL---VTISTDTALSQEALLRLAS 495 G L V + A +QE ++ LA+ Sbjct: 486 EGTLAGEVRPAGSAAETQERIIALAT 511 Lambda K H 0.319 0.135 0.381 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: 577 Number of extensions: 37 Number of successful extensions: 10 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: 495 Length of database: 537 Length adjustment: 35 Effective length of query: 460 Effective length of database: 502 Effective search space: 230920 Effective search space used: 230920 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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