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 RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Cup4G11:RR42_RS32900 Length = 502 Score = 338 bits (867), Expect = 3e-97 Identities = 190/492 (38%), Positives = 282/492 (57%), Gaps = 8/492 (1%) Query: 6 LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65 L + + K + GV AL D ++ G VH L G NGAGKS+ + +L G+ DAG Sbjct: 10 LFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGEFYH 69 Query: 66 NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPR-RAGCIVDNKALNRRT 124 +G+PV P++ + GIA+I QE +PY+ +A+NI+LGREPR R VD ++ Sbjct: 70 DGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIPGSVDAARMHAEA 129 Query: 125 RELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFK 184 R +LD L +V +P+HRL VAQ Q+VEIAKA S + +++++DEPT+A+ + E + LF Sbjct: 130 RRILDILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETEKLFA 189 Query: 185 AIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQEL 244 I RL A G ++Y+SHR++E+ + D +I RDG V + D D LV +VG+ Sbjct: 190 VIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDELVARMVGR-- 247 Query: 245 TRIDHKVGRECAAN---TCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNC 301 ++D RE +A L V N+S DI+LQ+R GEI+G+ GL+GSGRSE Sbjct: 248 -KVDMSYSRERSAQPGEVALDVRNVSADSGIADINLQVRAGEIVGLAGLVGSGRSEVARA 306 Query: 302 IYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYK 361 ++G G + + GK + G P G +L+ E RK GL L ++ N+ L+ + Sbjct: 307 VFGADPIRQGEIYIFGKRLTGG-PDRARELGAALIPESRKSEGLALIRTVRDNLLLAGLR 365 Query: 362 RLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLL 421 R A K LAE + RL+I T +SGGNQQK+V+ K L E + Sbjct: 366 RAFPARWYRADKAEALAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGKWLVAEAKLFI 425 Query: 422 CDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTIST 481 DEPTRGID GAK EI+ L+D V+ G +++SSE PE++++ DR V +GGR+ Sbjct: 426 FDEPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGRIAGEVA 485 Query: 482 DTALSQEALLRL 493 +++E +L+L Sbjct: 486 HAEMTEERILQL 497 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: 553 Number of extensions: 31 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: 502 Length adjustment: 34 Effective length of query: 461 Effective length of database: 468 Effective search space: 215748 Effective search space used: 215748 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