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 Ac3H11_609 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_609 Length = 505 Score = 320 bits (819), Expect = 1e-91 Identities = 188/500 (37%), Positives = 300/500 (60%), Gaps = 13/500 (2%) Query: 5 LLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDA--GS 62 +LL+ ++ K + GV AL L ++AG +HA+ G NGAGKST + +L G+ + G Sbjct: 1 MLLEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQ 60 Query: 63 ILLNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNR 122 IL +G +F ++ GI +I QEL +P +++AENI+LG E R G ++D A + Sbjct: 61 ILFDGQEREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNETARHG-VIDWMAAHS 119 Query: 123 RTRELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTL 182 R + LL + +P+ +L V + QLVEIAKA S +++I+DEPT+++ E+++Q L Sbjct: 120 RAQALLHKVGLGESPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNENDSQAL 179 Query: 183 FKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVE--SGRMADIDRDHLVRGIV 240 + L AQG + +SH+L+E++++AD ++ RDG+ V+ R + D +++ +V Sbjct: 180 LDLLLELKAQGITCILISHKLNEISRVADAITVLRDGSTVQMLDCREGPVSEDRVIQAMV 239 Query: 241 GQELT----RIDHKVGRECAANTCLQVDNLSRAGEFH--DISLQLRQGEILGIYGLMGSG 294 G+E++ + +VG + + R+ H I L +R+GEI+GI GLMG+G Sbjct: 240 GREMSDRYPQRQPQVGEIVFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIAGLMGAG 299 Query: 295 RSEFLNCIYGLTVAD--SGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSIL 352 R+E I+G + SG V L G+P+ + + ++ G++ VTEDRK +GLVL I Sbjct: 300 RTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLVLNEDIQ 359 Query: 353 SNIALSAYKRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKC 412 N +L+ +S S+I++ +E ++A+D ++L+I+ + ++ ++SGGNQQKVVL+K Sbjct: 360 FNTSLANLPGVSFASVIDSGQEHRVAQDYREKLRIRCSGVDQKTLNLSGGNQQKVVLSKW 419 Query: 413 LSTEPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFK 472 L T P L+ DEPTRGID GAK EIY L+ Q G IV+SSE PELL ++DRI V Sbjct: 420 LFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITDRIYVMN 479 Query: 473 GGRLVTISTDTALSQEALLR 492 GR V + SQE ++R Sbjct: 480 EGRFVAEMPTSEASQEKIMR 499 Score = 67.8 bits (164), Expect = 9e-16 Identities = 52/225 (23%), Positives = 102/225 (45%), Gaps = 15/225 (6%) Query: 27 LSLRAGSVHALCGGNGAGKSTFLSILMGIT--QRDAGSILLNGAPVQFNRPSEALAAGIA 84 L++R G + + G GAG++ + G + QR +G + L+G P+ + +A++ G+A Sbjct: 282 LNVRRGEIVGIAGLMGAGRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHGLA 341 Query: 85 MITQEL--------EPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTRELLDSLEFDVD 136 +T++ E I + T N+ ++D+ +R ++ + L Sbjct: 342 YVTEDRKGNGLVLNEDIQFNTSLANL----PGVSFASVIDSGQEHRVAQDYREKLRIRCS 397 Query: 137 ATSPMH-RLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTAQGAG 195 LS Q V ++K +V+I+DEPT I ++ I +L A+G Sbjct: 398 GVDQKTLNLSGGNQQKVVLSKWLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKC 457 Query: 196 IVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIV 240 ++ +S + EL I D + +G FV ++ ++ ++R IV Sbjct: 458 VIVISSEMPELLGITDRIYVMNEGRFVAEMPTSEASQEKIMRAIV 502 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: 586 Number of extensions: 27 Number of successful extensions: 9 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: 505 Length adjustment: 34 Effective length of query: 461 Effective length of database: 471 Effective search space: 217131 Effective search space used: 217131 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