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_086509530.1 BZY95_RS08595 ABC transporter ATP-binding protein
Query= uniprot:A0A1N7TX47 (495 letters) >NCBI__GCF_002151265.1:WP_086509530.1 Length = 269 Score = 106 bits (264), Expect = 1e-27 Identities = 79/267 (29%), Positives = 124/267 (46%), Gaps = 7/267 (2%) Query: 7 LQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLN 66 L ++ Y + + + LSL G V A+ G NG GKST L+ L + G++LL+ Sbjct: 6 LATRDLSLGYGRITIIDELALSLPTGQVTAIVGPNGCGKSTLLAGLARLHAPSHGAVLLD 65 Query: 67 GAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTRE 126 G +Q P+ LA +A++ QE +TVAE + GR+P + + + E Sbjct: 66 GQDIQ-QLPARELARRLALLPQEASAPEGLTVAELVRFGRQPHQGWLRQWSAEDQQVVHE 124 Query: 127 LLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAI 186 L + + D A P+ LS Q Q IA + ++++DEPTSA+ +F+ + Sbjct: 125 ALAAADVDELADRPLDTLSGGQRQRAWIAMTITQQTPLLLLDEPTSALDLGHQIEVFELV 184 Query: 187 RRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQELTR 246 RRL A G +V V H L+ + AD R G V +G ++ LVR + + T Sbjct: 185 RRLAAHGRTVVMVLHDLASACRYADHLVALRHGQLVAAGPPGEVVTTELVRQLYDIDCTL 244 Query: 247 IDHKVGRECAANTCLQVDNLSRAGEFH 273 I A L + N+ RA F+ Sbjct: 245 IPD------PATGSLLLANVRRAPRFN 265 Score = 60.1 bits (144), Expect = 9e-14 Identities = 42/204 (20%), Positives = 93/204 (45%), Gaps = 6/204 (2%) Query: 274 DISLQLRQGEILGIYGLMGSGRSEFLNCIYGLTVADSGSVTLQGKPMPIGLPKATINAGM 333 +++L L G++ I G G G+S L + L G+V L G+ + LP + + Sbjct: 23 ELALSLPTGQVTAIVGPNGCGKSTLLAGLARLHAPSHGAVLLDGQDIQ-QLPARELARRL 81 Query: 334 SLVTEDRKDSGLVLTGSILSNIALSAYKRLSSWSLINARKETQLAEDMVKRLQIKTTSLE 393 +L+ ++ G ++ + + W + ++ Q+ + + + + + Sbjct: 82 ALLPQEASAP----EGLTVAELVRFGRQPHQGWLRQWSAEDQQVVHEALAAADVDELA-D 136 Query: 394 LPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIV 453 P+ ++SGG +Q+ +A ++ + LL DEPT +D G + E++ L+ + G ++ Sbjct: 137 RPLDTLSGGQRQRAWIAMTITQQTPLLLLDEPTSALDLGHQIEVFELVRRLAAHGRTVVM 196 Query: 454 VSSEAPELLHLSDRIAVFKGGRLV 477 V + +D + + G+LV Sbjct: 197 VLHDLASACRYADHLVALRHGQLV 220 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: 298 Number of extensions: 16 Number of successful extensions: 5 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: 269 Length adjustment: 29 Effective length of query: 466 Effective length of database: 240 Effective search space: 111840 Effective search space used: 111840 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: 49 (23.5 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