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_106712778.1 CU102_RS19520 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A1N7TX47 (495 letters) >NCBI__GCF_003010955.1:WP_106712778.1 Length = 505 Score = 321 bits (822), Expect = 4e-92 Identities = 173/470 (36%), Positives = 275/470 (58%), Gaps = 3/470 (0%) Query: 5 LLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSIL 64 +LL A + K++ G AL L++R G +HAL G NGAGKST + +L G+ Q D G + Sbjct: 6 VLLAARGICKSFIGFRALDAVDLTIRRGEIHALLGENGAGKSTLIKVLTGVHQPDLGVME 65 Query: 65 LNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRT 124 L+G P+ +A GI + QE+ +P M+VA+N+++GR+P R G +D + + +R Sbjct: 66 LDGQPIHVRDTLQAQQLGIGTVYQEVNLLPNMSVADNLFVGRQPMRFG-FIDRRRMEKRA 124 Query: 125 RELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFK 184 RELL + +D +S + R SVA QLV IA+A +++I+DEPT+++ HE + LF Sbjct: 125 RELLSQYDLHIDVSSDLSRYSVAVQQLVAIARAVDMSGRILILDEPTASLDRHETEILFA 184 Query: 185 AIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQEL 244 +RRL +G GIV+++H L ++ +I D ++ R+G S + + + LV ++G+ L Sbjct: 185 TLRRLKERGLGIVFITHFLDQVYEICDRVTVLRNGKVAGSELTSQLPKMQLVSLMLGRAL 244 Query: 245 TRIDHKVGRECAANTCLQVD--NLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCI 302 + H V R+ Q + R+ L + +GE++G+ GL+GSGR+E + Sbjct: 245 AAVTHNVRRDRQEPETKQFSFKGMGRSRSVAPFDLDIGEGEVIGMAGLLGSGRTETARLL 304 Query: 303 YGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKR 362 +G+ AD+G + G P+ I P+ + G L EDRK G++ S+ NI L+ + Sbjct: 305 FGIDSADTGQAAVDGVPVRIRSPQDAVALGFGLCPEDRKTDGIIGDLSVRENIVLALQAQ 364 Query: 363 LSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLC 422 + + R++ LA+ VK L I+TT +E P+ +SGGNQQKV+LA+ L+T P L+ Sbjct: 365 RGWFKRLPRRQQVALADKFVKALDIRTTDIEKPIKFLSGGNQQKVILARWLATNPRFLIL 424 Query: 423 DEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFK 472 DEPTRGID GA EI L++Q G A +V+SSE E++ S R+ V + Sbjct: 425 DEPTRGIDVGAHAEIIALINQLCDDGMALLVISSEIEEIVAYSTRVVVLR 474 Score = 67.8 bits (164), Expect = 9e-16 Identities = 57/220 (25%), Positives = 96/220 (43%), Gaps = 27/220 (12%) Query: 27 LSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFNRPSEALAAGIAMI 86 L + G V + G G+G++ +L GI D G ++G PV+ P +A+A G + Sbjct: 279 LDIGEGEVIGMAGLLGSGRTETARLLFGIDSADTGQAAVDGVPVRIRSPQDAVALGFGLC 338 Query: 87 TQELEP---IPYMTVAENI---------WLGREPRRAGCIVDNK---ALNRRTRELLDSL 131 ++ + I ++V ENI W R PRR + +K AL+ RT Sbjct: 339 PEDRKTDGIIGDLSVRENIVLALQAQRGWFKRLPRRQQVALADKFVKALDIRT------- 391 Query: 132 EFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTA 191 D P+ LS Q V +A+ + + + +I+DEPT I + I +L Sbjct: 392 ---TDIEKPIKFLSGGNQQKVILARWLATNPRFLILDEPTRGIDVGAHAEIIALINQLCD 448 Query: 192 QGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADID 231 G ++ +S + E+ + + RD V+ G +A D Sbjct: 449 DGMALLVISSEIEEIVAYSTRVVVLRDR--VQRGELAGDD 486 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: 544 Number of extensions: 20 Number of successful extensions: 6 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 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