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_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein
Query= uniprot:A0A1N7TX47 (495 letters) >NCBI__GCF_900167125.1:WP_078716498.1 Length = 514 Score = 226 bits (577), Expect = 1e-63 Identities = 153/481 (31%), Positives = 255/481 (53%), Gaps = 19/481 (3%) Query: 6 LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65 L+ + + K + V A D L++ G V AL G NGAGKST +S+L G Q DAG+I L Sbjct: 24 LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIAL 83 Query: 66 NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTR 125 +G PV+F+ +A+ AGI M+ Q + MTVAEN+ LG+E ++ K + R + Sbjct: 84 DGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQE---GSFFLNPKEMRNRVQ 140 Query: 126 ELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKA 185 EL D+D + + LS+ + Q VEI K D +V+I DEPT+ + E LF+A Sbjct: 141 ELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEA 200 Query: 186 IRRLTAQGAGIVYVSHRLSELAQIADDYSIFR----DGAFVESGRMADIDRDHLVRGIVG 241 + ++ QG IV++SH+L E+ +AD+ +I R +G F ES + D L +VG Sbjct: 201 LWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKAD---LACRMVG 257 Query: 242 QELTRIDHKVGRECA--ANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFL 299 +E+ +V RE + LQV NL+ G DI+ L QGE++ + G+ G+G+ + Sbjct: 258 KEVLL---EVDREAMPHGDAVLQVRNLTGIG-LEDITFDLHQGEVVAVVGVAGNGQKALV 313 Query: 300 NCIYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSA 359 I GL ++ + GK K + ++ + EDR +++ N+ L+ Sbjct: 314 EAICGLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLLTT 373 Query: 360 YKRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVC 419 + + ++ +K + +++K+ I+ + +SGGN QK VLA+ L P Sbjct: 374 RQGFARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRL 433 Query: 420 LLCDEPTRGIDEGAKQEIY-HLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVT 478 ++ ++PT+G+D A ++++ HLL R ++V+ + E L L+DR+AV GR + Sbjct: 434 IVAEQPTQGLDIAATEQVWNHLL--AAREMAGILLVTGDLNEALQLADRVAVIYRGRFMD 491 Query: 479 I 479 + Sbjct: 492 V 492 Score = 69.3 bits (168), Expect = 3e-16 Identities = 49/216 (22%), Positives = 103/216 (47%), Gaps = 8/216 (3%) Query: 274 DISLQLRQGEILGIYGLMGSGRSEFLNCIYGLTVADSGSVTLQGKPMPIGLPKATINAGM 333 DISL + G + + G G+G+S ++ + G D+G++ L GKP+ + I AG+ Sbjct: 42 DISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIALDGKPVRFSSARDAIEAGI 101 Query: 334 SLVTEDRKDSGLVLTGSILSNIALSAYKRLSSWSLINARKETQLAEDMVKRLQIKTTSLE 393 +V + LV + ++ N+ L +N ++ +++ R + Sbjct: 102 GMVYQHFM---LVESMTVAENVLLGQEGSF----FLNPKEMRNRVQELSVRYGLDIDPAA 154 Query: 394 LPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIV 453 V+ +S G +Q+V + K L + L+ DEPT + ++ L + G + + Sbjct: 155 R-VSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEALWKIAEQGKSIVF 213 Query: 454 VSSEAPELLHLSDRIAVFKGGRLVTISTDTALSQEA 489 +S + E+L ++D IA+ + GR+ +++ ++ +A Sbjct: 214 ISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKA 249 Score = 39.3 bits (90), Expect = 3e-07 Identities = 42/213 (19%), Positives = 92/213 (43%), Gaps = 6/213 (2%) Query: 22 LRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFNRPSEALAA 81 L D L G V A+ G G G+ + + G+ + ++ + G + + Sbjct: 286 LEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSWKN 345 Query: 82 GIAMITQE---LEPIPYMTVAENIWLG-REPRRAGCIVDNKALNRRTRELLDSLEFDVDA 137 +A I ++ L + + +N+ L R+ G +D K R T EL+ + Sbjct: 346 SLAYIPEDRLGLATCRNLNLVDNLLLTTRQGFARGPWLDKKKAARDTTELIKKFDIRPGR 405 Query: 138 TSPMH-RLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTAQGAGI 196 + + +LS +Q +A+ ++++ ++PT + + ++ + + AGI Sbjct: 406 IAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAATEQVWNHLLA-AREMAGI 464 Query: 197 VYVSHRLSELAQIADDYSIFRDGAFVESGRMAD 229 + V+ L+E Q+AD ++ G F++ ++D Sbjct: 465 LLVTGDLNEALQLADRVAVIYRGRFMDVFSVSD 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: 491 Number of extensions: 28 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 495 Length of database: 514 Length adjustment: 34 Effective length of query: 461 Effective length of database: 480 Effective search space: 221280 Effective search space used: 221280 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 Apr 09 2024. 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