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_RS14860 BWI76_RS14860 ABC transporter
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Koxy:BWI76_RS14860 Length = 510 Score = 350 bits (899), Expect = e-101 Identities = 186/492 (37%), Positives = 303/492 (61%), Gaps = 3/492 (0%) Query: 1 MARPLLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDA 60 ++ P LL+ E ++K Y AL + R L AG VHAL G NGAGKST + IL G QRD+ Sbjct: 4 ISSPPLLRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDS 63 Query: 61 GSILLNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKAL 120 G I ++G + P +A GIA+I QEL +P MTVAEN++LG+EP I+D K + Sbjct: 64 GVIFIDGQAIDIRTPRDARKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGILDRKRM 123 Query: 121 NRRTRELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQ 180 +R +E L+ + D+D +P+ LS+ + Q+VEIA+A S + +V+++DEPT+A+ E Sbjct: 124 HREAKEKLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETL 183 Query: 181 TLFKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIV 240 L++ I ++ G G+VY+SHR+ E+ Q+A+ ++FRDG ++ + + ++ +VR +V Sbjct: 184 QLYRLIAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVRMMV 243 Query: 241 GQELTRIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLN 300 G+++ + R + L+V +L+ + +S ++ GE++ + GL+GSGR+E Sbjct: 244 GRQIVDLYQHEPR-TPGDVLLEVRDLAGSAT-GPVSFEVSAGEVVSMSGLVGSGRTEVAR 301 Query: 301 CIYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAY 360 ++G GSV L G+ P A I G+ +VTEDRK GL L S+ NI +S+ Sbjct: 302 LLFGADPRSQGSVRLAGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDISSL 361 Query: 361 KRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCL 420 + ++ + + ++RL+++ ++ELPV+++SGGNQQK LA+ L + L Sbjct: 362 DNFVAGGVVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDSRLL 421 Query: 421 LCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLV-TI 479 + DEPTRG+D GAK+EIY L+D+ R G A +V+SS+ PE + +SDR+ V +GGR+V + Sbjct: 422 ILDEPTRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVHQL 481 Query: 480 STDTALSQEALL 491 + +A +E +L Sbjct: 482 PSCSATEEEVML 493 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: 627 Number of extensions: 30 Number of successful extensions: 6 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: 510 Length adjustment: 34 Effective length of query: 461 Effective length of database: 476 Effective search space: 219436 Effective search space used: 219436 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