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_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A1N7TX47 (495 letters) >NCBI__GCF_003046325.1:WP_069332735.1 Length = 499 Score = 324 bits (830), Expect = 5e-93 Identities = 195/489 (39%), Positives = 278/489 (56%), Gaps = 4/489 (0%) Query: 6 LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65 +L V++ + V L D LR G VHAL G NGAGKST + IL G AG +LL Sbjct: 5 VLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVLL 64 Query: 66 NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTR 125 +G PV F EA AAG+ MI QE +TV ENI+LGRE +R G +D++A+ +R Sbjct: 65 DGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKR-GPFLDHRAMQAESR 123 Query: 126 ELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKA 185 LL+ L VD + + LSV Q+VEIAKA +V+IMDEPT+ + E TL + Sbjct: 124 RLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLLEQ 183 Query: 186 IRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQELT 245 + RL A G I+Y SH+L E+A+IAD ++ RDG V + + D + +VG+EL+ Sbjct: 184 VDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGRELS 243 Query: 246 RIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYGL 305 + A L+V L+ G D S LR+GE+LG GL+GSGR+E + I GL Sbjct: 244 GL-FPPKSSPAPEPVLEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGRTELMEGIVGL 302 Query: 306 TVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRLSS 365 A +G V ++G P+P A AG+ +TEDRK+ GL+L + N+ L A R Sbjct: 303 RPA-TGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTLLALDRFGR 361 Query: 366 WSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEP 425 + A +E L + + I+ + S+SGGNQQK++LAK + EP ++ DEP Sbjct: 362 VLIDKAAEERALTQ-AISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAEPRVVIIDEP 420 Query: 426 TRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDTAL 485 TRGID G KQ+IY + + G + IVVSSE PE++ L++R+ V GR+ A+ Sbjct: 421 TRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRIAGEVEGEAI 480 Query: 486 SQEALLRLA 494 ++E ++RLA Sbjct: 481 TEENIVRLA 489 Score = 70.9 bits (172), Expect = 1e-16 Identities = 56/224 (25%), Positives = 101/224 (45%), Gaps = 5/224 (2%) Query: 22 LRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFNRPSEALAA 81 +RD +LR G V G G+G++ + ++G+ G + + G+P+ S A AA Sbjct: 269 VRDASFTLRRGEVLGFAGLVGSGRTELMEGIVGLRPA-TGEVRMEGSPLPHASVSAARAA 327 Query: 82 GIAMITQELEPIPYMT---VAENIWLGREPRRAGCIVDNKALNRRTRELLDSLEFDV-DA 137 G+ +T++ + + + EN+ L R ++D A R + + + V D Sbjct: 328 GLVYLTEDRKEKGLLLGKPLGENLTLLALDRFGRVLIDKAAEERALTQAISDFDIRVGDR 387 Query: 138 TSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTAQGAGIV 197 LS Q + +AK + +V+I+DEPT I Q ++ I RL A+G ++ Sbjct: 388 GISAGSLSGGNQQKLLLAKTMLAEPRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVI 447 Query: 198 YVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVG 241 VS L E+ +A+ + G I +++VR +G Sbjct: 448 VVSSELPEVIGLANRVVVMSAGRIAGEVEGEAITEENIVRLAMG 491 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: 595 Number of extensions: 41 Number of successful extensions: 10 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: 499 Length adjustment: 34 Effective length of query: 461 Effective length of database: 465 Effective search space: 214365 Effective search space used: 214365 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