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 BPHYT_RS19720 BPHYT_RS19720 arabinose ABC transporter ATP-binding protein
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__BFirm:BPHYT_RS19720 Length = 515 Score = 351 bits (900), Expect = e-101 Identities = 192/489 (39%), Positives = 292/489 (59%), Gaps = 3/489 (0%) Query: 7 LQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLN 66 L+ + + + GV AL L +R G VH L G NGAGKST L +L G+ Q AG++ L+ Sbjct: 26 LRLDGITVRFPGVLALDQVSLEVRRGEVHGLMGENGAGKSTLLKVLSGVNQPAAGTLSLD 85 Query: 67 GAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTRE 126 G QF A+AAG+A+I QEL +P +TVAEN+ LG P R G I+D KAL R Sbjct: 86 GVEQQFITTKAAIAAGVAIIYQELHLVPELTVAENLMLGALPNRFG-ILDEKALVARAVR 144 Query: 127 LLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAI 186 L+ L +D + + LS+ Q Q++EI KA D +V+ DEPTS++ E LF+ I Sbjct: 145 ELERLGEKIDPSQQVKNLSIGQRQMIEIGKALMRDARVIAFDEPTSSLSSRETTQLFRII 204 Query: 187 RRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMAD-IDRDHLVRGIVGQELT 245 R L A+G I+YV+HR+ E+ ++ D ++FRDG +++ + +DRD L+ +VG+ + Sbjct: 205 RALKAEGRAIIYVTHRMDEVYELCDRVTVFRDGRRIDTFEAGEGLDRDRLISCMVGRSIA 264 Query: 246 RIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYGL 305 + R+ + L V + G S R+GEI+G +GL+G+GRSE + IYG Sbjct: 265 DVYGYRSRDLG-DVQLDVKEMMGRGLREPASFTARKGEIVGFFGLVGAGRSELMKLIYGA 323 Query: 306 TVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRLSS 365 D+G + L+GK + P+ + AG++L EDRK G+V S+ N+ +S + S Sbjct: 324 VKPDAGEIALKGKRVRFATPRDAVRAGVALCPEDRKQEGIVSIASVSDNLNISCRRHFSR 383 Query: 366 WSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEP 425 ++++N RKE Q A++ + +L IKT + + P+ ++SGGNQQKV+L++ L+ + L DEP Sbjct: 384 FNVLNGRKEAQTAKEFIGKLAIKTRNGDTPIGTLSGGNQQKVILSRWLAEDIDVFLMDEP 443 Query: 426 TRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDTAL 485 TRGID GA+ EIY LL G IVVSS+ E++ ++DR+ V K GR+V Sbjct: 444 TRGIDVGARSEIYGLLYGLAEAGRTVIVVSSDLAEVIGVADRVIVMKEGRIVGDLPKAQA 503 Query: 486 SQEALLRLA 494 + +AL++LA Sbjct: 504 TPDALIKLA 512 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: 569 Number of extensions: 26 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: 515 Length adjustment: 34 Effective length of query: 461 Effective length of database: 481 Effective search space: 221741 Effective search space used: 221741 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