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 16258 b2149 fused methyl-galactoside transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Keio:16258 Length = 506 Score = 346 bits (888), Expect = e-99 Identities = 194/498 (38%), Positives = 302/498 (60%), Gaps = 15/498 (3%) Query: 6 LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65 LL+ + K++ GV AL + L +R S+HAL G NGAGKST L L GI Q+D+G+IL Sbjct: 13 LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72 Query: 66 NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTR 125 G + F+ EAL GI+M+ QEL + +V +N+WLGR P + G VD + R T+ Sbjct: 73 QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTK-GMFVDQDKMYRETK 131 Query: 126 ELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKA 185 + D L+ D+D + + LSV+Q+Q++EIAKAFS++ +++IMDEPTS++ E E LF Sbjct: 132 AIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191 Query: 186 IRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQELT 245 IR+L +G GIVY+SH++ E+ Q+ D+ ++ RDG ++ + +A + D ++ +VG+ L Sbjct: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLN 251 Query: 246 -RIDHKVGRECAANTCLQVDNLS--RAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCI 302 R K + L+V NL+ R D+S L +GEILGI GL+G+ R++ + + Sbjct: 252 QRFPDKENK--PGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETL 309 Query: 303 YGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGL-----VLTGSILSNIAL 357 +G+ +G++TL GK + IN G +LVTE+R+ +G+ + S++SNI Sbjct: 310 FGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNI-- 367 Query: 358 SAYKRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEP 417 YK + L++ + + ++ +++KT + S+SGGNQQKV++ + L T+P Sbjct: 368 RNYK--NKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQP 425 Query: 418 VCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLV 477 L+ DEPTRGID GAK EIY L+ + + G I++SSE PELL ++DRI V G + Sbjct: 426 EILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVS 485 Query: 478 TISTDTALSQEALLRLAS 495 I +Q +LRLAS Sbjct: 486 GIVDTKTTTQNEILRLAS 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: 545 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: 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