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 WP_041936920.1 RL_RS31840 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A1N7TX47 (495 letters) >NCBI__GCF_000009265.1:WP_041936920.1 Length = 511 Score = 360 bits (923), Expect = e-104 Identities = 200/492 (40%), Positives = 297/492 (60%), Gaps = 1/492 (0%) Query: 4 PLLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSI 63 P +L+ +++ + GV AL + ++L G+V AL G NGAGKST + IL GI + + G I Sbjct: 18 PAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEI 77 Query: 64 LLNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRR 123 L++G PV F A+ AG+ I QE +TVAENI+LG PR +D +A+N R Sbjct: 78 LVDGQPVTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRLRTIDWQAMNSR 137 Query: 124 TRELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLF 183 + LL +LE ++D T + S+AQ LV IA+A S + +++IMDEPT+A+ E LF Sbjct: 138 AKALLTALESNIDPTIRLKDFSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLF 197 Query: 184 KAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQE 243 + +R L +G I+++SH+ E+ +IADD+ +FRDG V GR+ + +D +VR +VG++ Sbjct: 198 RIVRGLKEKGKAILFISHKFDEVYEIADDFVVFRDGRAVGQGRLKETPQDEIVRMMVGRD 257 Query: 244 LTRIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIY 303 + KV L++ N S EF DIS LRQGEILGIYGL+G+GRSE ++ Sbjct: 258 VENAFPKVD-VAFGGPVLEIRNYSHRTEFRDISFTLRQGEILGIYGLIGAGRSELSQSLF 316 Query: 304 GLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRL 363 G+T SG + L+G+ + I P+ I AG+ V E+R GL L I N+ L + R Sbjct: 317 GITRPLSGKMMLEGREITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLTRT 376 Query: 364 SSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCD 423 S + A +E LA +RL ++ +L +PV ++SGGNQQKVV+ K L+T P ++ D Sbjct: 377 SRRGFLRAAEEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILD 436 Query: 424 EPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDT 483 EPT+GID G+K ++ + + G + I+VSSE PE++ +SDR+ V K G I Sbjct: 437 EPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLAAGIFERA 496 Query: 484 ALSQEALLRLAS 495 LS EAL+R A+ Sbjct: 497 ELSPEALVRAAT 508 Score = 78.2 bits (191), Expect = 6e-19 Identities = 66/233 (28%), Positives = 102/233 (43%), Gaps = 9/233 (3%) Query: 16 YAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFNRP 75 Y+ RD +LR G + + G GAG+S L GIT+ +G ++L G + + P Sbjct: 279 YSHRTEFRDISFTLRQGEILGIYGLIGAGRSELSQSLFGITRPLSGKMMLEGREITIHSP 338 Query: 76 SEALAAGIAMITQELE------PIPYMTVAENIWLGREPRRAGC-IVDNKALNRRTRELL 128 +A+ AGI + +E P+P L R RR + AL R+ E L Sbjct: 339 QDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLTRTSRRGFLRAAEEFALARKYAERL 398 Query: 129 DSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRR 188 D + P+ LS Q V I K + +V+I+DEPT I + I Sbjct: 399 DLRAAALSV--PVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISE 456 Query: 189 LTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVG 241 L A+G I+ VS L E+ ++D + ++G A++ + LVR G Sbjct: 457 LAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLAAGIFERAELSPEALVRAATG 509 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: 22 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 495 Length of database: 511 Length adjustment: 34 Effective length of query: 461 Effective length of database: 477 Effective search space: 219897 Effective search space used: 219897 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 24 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