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_02331 H281DRAFT_02331 L-arabinose ABC transporter ATP-binding protein
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Burk376:H281DRAFT_02331 Length = 520 Score = 353 bits (907), Expect = e-102 Identities = 195/489 (39%), Positives = 292/489 (59%), Gaps = 3/489 (0%) Query: 7 LQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLN 66 LQ + + + GV AL L +R G VH L G NGAGKST L +L G+ Q AG++ L+ Sbjct: 31 LQLDGITVRFPGVLALDQVSLEVRRGEVHGLMGENGAGKSTLLKVLSGVNQPAAGTLSLD 90 Query: 67 GAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTRE 126 G QF A+AAG+A+I QEL +P +TVAEN+ LG P R G ++D KAL R Sbjct: 91 GVEQQFTTTKAAIAAGVAIIYQELHLVPELTVAENLMLGALPNRFG-VLDEKALVARAVR 149 Query: 127 LLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAI 186 L+ L +D + + LS+ Q Q++EI KA D +V+ DEPTS++ E LF+ I Sbjct: 150 ELERLGEKIDPSQQVKNLSIGQRQMIEIGKALMRDARVIAFDEPTSSLSSRETTQLFRII 209 Query: 187 RRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVES-GRMADIDRDHLVRGIVGQELT 245 R L A+G I+YV+HR+ E+ ++ D ++FRDG +++ A +DRD L+ +VG+ + Sbjct: 210 RALRAEGRAIIYVTHRMDEVYELCDRVTVFRDGRRIDTFDAGAGLDRDRLISCMVGRSIA 269 Query: 246 RIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYGL 305 + R+ + L V L G + R+GEI+G +GL+G+GRSE + IYG Sbjct: 270 DVYGYRTRD-VGDVQLDVKGLMGPGLREPATFSARKGEIVGFFGLVGAGRSELMKLIYGA 328 Query: 306 TVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRLSS 365 +G +TL+GK + P+ + AG++L EDRK G+V S+ N+ +S + S Sbjct: 329 VKPTAGDITLKGKQVRFATPRDAVRAGVALCPEDRKQEGIVSIASVSDNLNISCRRHFSR 388 Query: 366 WSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEP 425 ++++N RKE Q A++ + +L IKT + E P+ ++SGGNQQKV+L++ L+ + L DEP Sbjct: 389 FNVLNGRKEAQTAKEFIGKLAIKTRNGETPIGTLSGGNQQKVILSRWLAEDIDVFLMDEP 448 Query: 426 TRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDTAL 485 TRGID GA+ EIY LL G IVVSS+ E++ ++DR+ V K GRLV Sbjct: 449 TRGIDVGARSEIYGLLYGLADAGRTVIVVSSDLAEVIGVTDRVIVMKEGRLVGDLPKAQA 508 Query: 486 SQEALLRLA 494 + +AL++LA Sbjct: 509 TPDALIKLA 517 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: 603 Number of extensions: 31 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: 520 Length adjustment: 34 Effective length of query: 461 Effective length of database: 486 Effective search space: 224046 Effective search space used: 224046 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