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 SM_b20503 SM_b20503 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Smeli:SM_b20503 Length = 512 Score = 366 bits (939), Expect = e-105 Identities = 203/498 (40%), Positives = 308/498 (61%), Gaps = 6/498 (1%) Query: 1 MARPLLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDA 60 M +L+ +V+K + V AL L G VHALCG NGAGKST ++++ G+ Q Sbjct: 1 MTSETVLEIRNVSKHFGAVKALTAVDFRLARGEVHALCGENGAGKSTLMNVIAGVLQPSE 60 Query: 61 GSILLNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKAL 120 G +L+ GAPV+ P+ A + GIA++ QE+ P T+AEN+++ RR +++ L Sbjct: 61 GEVLIEGAPVKIASPAVAQSLGIALVHQEIALCPDATIAENMFMAATNRRRSALMNYAQL 120 Query: 121 NRRTRELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQ 180 R + +++ L +D + + L ++ QLVEIAKA + DC+V+I DEPT+A+ E EAQ Sbjct: 121 ERDAQAVMNRLA-PIDVSQKVGDLPISSQQLVEIAKALTLDCRVLIFDEPTAALTETEAQ 179 Query: 181 TLFKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIV 240 LF IR L A+G I+Y+SHR++E+ + D ++FRDG +V + ++D+ D +VR +V Sbjct: 180 VLFGIIRDLKARGISIIYISHRMAEVFSLCDRVTVFRDGRYVATEMVSDVTPDDVVRLMV 239 Query: 241 GQELTRI--DHKVGRECAANTCLQVDNLSRAGE-FHDISLQLRQGEILGIYGLMGSGRSE 297 G+E++++ D + E L V +L GE F D+S +LR GEILG+ GL+GSGR+E Sbjct: 240 GREISQLYPDKQPSSERLGEPILSVRDLG--GERFRDVSFELRYGEILGVGGLIGSGRTE 297 Query: 298 FLNCIYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIAL 357 I L G + L K + + AG+ ++EDRK SG+ L SI NIA Sbjct: 298 IAEGICALRPVTQGEIRLHDKVLRLRRYSDAAKAGVVYLSEDRKGSGVFLDLSIAQNIAA 357 Query: 358 SAYKRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEP 417 K L+S L+N+R+E LAED+ +RL ++ +++PV+S+SGGNQQKV +AK L+ +P Sbjct: 358 LDLKALTSLGLLNSREERALAEDLTRRLGVRMGGVDMPVSSLSGGNQQKVAIAKQLAVDP 417 Query: 418 VCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLV 477 +L DEPTRGID GAK EI+ LL + R G +V+SSE PEL+ L DR+ V + GR+ Sbjct: 418 KVILMDEPTRGIDVGAKSEIHRLLRELARAGIGILVISSELPELIGLCDRVLVVREGRIA 477 Query: 478 TISTDTALSQEALLRLAS 495 + +++E ++RLAS Sbjct: 478 GEVSGNEMTEEVIMRLAS 495 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: 593 Number of extensions: 25 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: 512 Length adjustment: 34 Effective length of query: 461 Effective length of database: 478 Effective search space: 220358 Effective search space used: 220358 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