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_RS19640 BWI76_RS19640 galactose/methyl galactoside ABC transporter ATP-binding protein MglA
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Koxy:BWI76_RS19640 Length = 506 Score = 349 bits (896), Expect = e-100 Identities = 196/495 (39%), Positives = 301/495 (60%), Gaps = 9/495 (1%) Query: 6 LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65 LL+ ++ K++ GV AL + L +R S+HAL G NGAGKST L L GI Q+D+GSIL Sbjct: 13 LLEMTNINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSILF 72 Query: 66 NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTR 125 G + F+ EAL GI+M+ QEL + +V +N+WLGR P + G VD + R T+ Sbjct: 73 QGQEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTK-GVFVDQDKMYRDTK 131 Query: 126 ELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKA 185 + D L+ D+D + + LSV+Q+Q++EIAKAFS++ +++IMDEPTS++ E E LFK Sbjct: 132 AIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFKI 191 Query: 186 IRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQELT 245 IR+L +G GIVY+SH++ E+ Q+ D+ +I RDG ++ + + +D D ++ +VG+ L Sbjct: 192 IRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVGRSLN 251 Query: 246 -RIDHKVGRECAANTCLQVDNLS--RAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCI 302 R +K + L+V NL+ R DIS L +GEILGI GL+G+ R++ + + Sbjct: 252 QRFPNKENK--PGEVILEVRNLTSLRQPSIRDISFDLHKGEILGIAGLVGAKRTDIVETL 309 Query: 303 YGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKR 362 +G+ G++ L GK + IN G +LVTE+R+ +G+ I N +S K+ Sbjct: 310 FGIREKAGGTIRLHGKKINNHSANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIKK 369 Query: 363 LSS--WSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCL 420 + L N+R ++ + ++ +++KT + S+SGGNQQKV++ + L T+P L Sbjct: 370 YKNKVGLLDNSRMKSD-TQWVIDSMRVKTPGQHTQIGSLSGGNQQKVIIGRWLLTQPEIL 428 Query: 421 LCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTIS 480 + DEPTRGID GAK EIY L+ + + I++SSE PELL ++DRI V G + I Sbjct: 429 MLDEPTRGIDVGAKFEIYQLIAELAKKDKGIIIISSEMPELLGITDRILVMSNGLVAGIV 488 Query: 481 TDTALSQEALLRLAS 495 +Q +LRLAS Sbjct: 489 ETKTTTQNEILRLAS 503 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: 558 Number of extensions: 24 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: 506 Length adjustment: 34 Effective length of query: 461 Effective length of database: 472 Effective search space: 217592 Effective search space used: 217592 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