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 BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Koxy:BWI76_RS07240 Length = 494 Score = 413 bits (1062), Expect = e-120 Identities = 225/490 (45%), Positives = 315/490 (64%), Gaps = 3/490 (0%) Query: 7 LQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLN 66 L+AE ++K + GV AL + L +R G+VHAL G NGAGKST + L+GI + D G+I + Sbjct: 6 LEAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVK 65 Query: 67 GAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTRE 126 G PVQF +AL +GI+MI QEL +P+MTVAENIWLGREP + G VD++ L R+T++ Sbjct: 66 GEPVQFQDTMDALRSGISMIHQELNLVPHMTVAENIWLGREPMKYG-FVDHRQLARQTQD 124 Query: 127 LLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAI 186 LLD L + A + LS+A Q+VEIAKA S + ++IMDEPTSA+ E E LF I Sbjct: 125 LLDKLNIRLSADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTII 184 Query: 187 RRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQELTR 246 R L QG I+Y+SH++ E+ I D+ S+FRDG +V S + + R L+ +VG+ELT+ Sbjct: 185 RDLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQMVGRELTQ 244 Query: 247 IDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYGLT 306 + K L V NLSR G FHDI+ +R+GEILG+ GL+G+GRSE + ++G+ Sbjct: 245 LFPKF-NNAIGEEVLTVRNLSRKGAFHDINFSVRRGEILGVAGLVGAGRSEVMESLFGME 303 Query: 307 VADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIAL-SAYKRLSS 365 ADSG V + G P+ I P I GM+L+TEDRK SGL L S+L N+++ + + Sbjct: 304 KADSGEVLIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSIVKMPEYIGK 363 Query: 366 WSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEP 425 + K + + ++RL IKT +++ + ++SGGNQQKV++A+ L +P L+ DEP Sbjct: 364 TGFVQHLKMAEDCMEQIRRLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPKILILDEP 423 Query: 426 TRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDTAL 485 TRGID GAK EIYHL+ + G A I+VSSE PE+L +SDR+ V GR+ I Sbjct: 424 TRGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHEGRITGILDKEDA 483 Query: 486 SQEALLRLAS 495 QE +L LAS Sbjct: 484 DQETILSLAS 493 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: 624 Number of extensions: 20 Number of successful extensions: 8 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: 494 Length adjustment: 34 Effective length of query: 461 Effective length of database: 460 Effective search space: 212060 Effective search space used: 212060 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