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 H281DRAFT_00426 H281DRAFT_00426 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Burk376:H281DRAFT_00426 Length = 503 Score = 357 bits (915), Expect = e-103 Identities = 201/492 (40%), Positives = 290/492 (58%), Gaps = 2/492 (0%) Query: 6 LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65 L+ + ++K++ GV AL D + L G VHAL G NGAGKST + IL G+ RD+G ILL Sbjct: 4 LISVKKLSKSFPGVRALHDVQFDLVEGEVHALMGENGAGKSTLMKILAGVYTRDSGEILL 63 Query: 66 NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPR-RAGCIVDNKALNRRT 124 G PV+ P +A AAGI +I QEL+ + ++TVA+NI++GREPR R G +D LN + Sbjct: 64 GGQPVELQSPRDAQAAGIGIIHQELQLMNHLTVAQNIFIGREPRGRLGLFLDEDKLNAKA 123 Query: 125 RELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFK 184 RE+L + ++D + + L+VA Q+VEIAKA S D +V+IMDEPTSA+ + E LF+ Sbjct: 124 REILSRMHVNIDPRAMVGNLTVASQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAELFR 183 Query: 185 AIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQEL 244 IR L +G G+VY+SH++ EL QIAD ++ RDG +V + AD + ++ +VG+ L Sbjct: 184 IIRELKQRGVGVVYISHKMDELKQIADRVTVLRDGEYVATVAAADTSVEAIIGMMVGRTL 243 Query: 245 TRIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYG 304 + + L+V NL D+S LR+GEILG GLMG+GR+E ++G Sbjct: 244 SDVAPAGRAASQGEIALEVRNLHAGPLVRDVSFTLRKGEILGFAGLMGAGRTEVARAVFG 303 Query: 305 LTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRLS 364 +SG + ++G I P + G+ ++EDRK GL + SNI +S + Sbjct: 304 ADPVESGEIFVKGAKASIRTPSDAVAHGIGYLSEDRKRFGLATGMDVESNIVMSNLRNFL 363 Query: 365 SWSLINAR-KETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCD 423 S + R + + A + L I+T S V +SGGNQQK+V+AK L + L D Sbjct: 364 SLNFFLRRARMRRRASHFINLLAIRTPSAAQQVRLLSGGNQQKIVIAKWLERDCDVLFFD 423 Query: 424 EPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDT 483 EPTRGID GAK EIY LL G A +++SSE PE+L +SDR+ V GR+ Sbjct: 424 EPTRGIDVGAKSEIYKLLRSLADEGKAIVMISSELPEILRMSDRVVVMCEGRITGELPAE 483 Query: 484 ALSQEALLRLAS 495 +QE ++ LA+ Sbjct: 484 QATQERIMHLAT 495 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: 570 Number of extensions: 24 Number of successful extensions: 7 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: 503 Length adjustment: 34 Effective length of query: 461 Effective length of database: 469 Effective search space: 216209 Effective search space used: 216209 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