Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate H281DRAFT_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Burk376:H281DRAFT_02712 Length = 505 Score = 166 bits (420), Expect = 9e-46 Identities = 91/243 (37%), Positives = 160/243 (65%), Gaps = 3/243 (1%) Query: 5 LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPD-RGDLVF 63 LE+R++ ++F VKALD V++EI GEV+AL G+NGAGKSTL+KI++G + PD G ++ Sbjct: 10 LEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPGGTILV 69 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKI-FLNKKKMMEESK 122 EG++V + AR+LG+ IYQ+LA++ +L + NIFLARE ++ +++ +M E++ Sbjct: 70 EGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRPRMYREAR 129 Query: 123 KLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLE 182 ++L ++ + I D +V LS GQ+Q + +A+A+ +K I+MDEPTA+LS E +L Sbjct: 130 EVLATIDMDI-DPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETSVLLG 188 Query: 183 LARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTSFAL 242 + + L+++ + V+ I+H + + +E+ADR+ VL G+ + + E + +M + L Sbjct: 189 IVKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVRLMVAREL 248 Query: 243 GKV 245 ++ Sbjct: 249 SEL 251 Score = 99.4 bits (246), Expect = 1e-25 Identities = 64/240 (26%), Positives = 127/240 (52%), Gaps = 9/240 (3%) Query: 5 LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64 L ++ V K+ ++ +S +++GEV+ + G G+G++ ++++I G + G + E Sbjct: 270 LSLKPVRKAEPRIR---DISFTLHRGEVLGIAGLVGSGRTEIMEMIFGM-RACTGSVKIE 325 Query: 65 GKKVIFNSPNDARSLGIETIYQDL---ALIPDLPIYYNIFLAR--EVTNKIFLNKKKMME 119 GK V +P+DA GI + +D LI + + N L + F+ + E Sbjct: 326 GKPVSIRNPHDAIRSGIGFVTEDRKAQGLILGMTVRENFSLTHLERYSPFQFVQHARERE 385 Query: 120 ESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARK 179 ++ + L I+ P + KV NLSGG +Q + +A+ V S K++++DEPT + V + Sbjct: 386 SCRRFVRMLGIKTPGVEQKVVNLSGGNQQKIVIAKWVARSPKVLIVDEPTRGIDVGAKAE 445 Query: 180 VLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTS 239 V L L +G+GV++I+ ++++ V+DRI + G+I + + + E++ + T+ Sbjct: 446 VHALIARLAAEGIGVIVISSDLLEVLAVSDRILTVREGRISGELSRAQASQEKVMALATA 505 Lambda K H 0.318 0.137 0.371 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: 254 Number of extensions: 14 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: 251 Length of database: 505 Length adjustment: 29 Effective length of query: 222 Effective length of database: 476 Effective search space: 105672 Effective search space used: 105672 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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