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 N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 311 bits (798), Expect = 3e-89 Identities = 180/478 (37%), Positives = 277/478 (57%), Gaps = 5/478 (1%) Query: 2 ARPLLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAG 61 ARP++LQA + K + AL L+LRAG VHAL G NGAGKST + +L G+ + D G Sbjct: 8 ARPVVLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRG 67 Query: 62 SILLNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGC-IVDNKAL 120 S+ L+G + + P EA GI + QE+ P ++VAEN++ GR PRR ++D + + Sbjct: 68 SVELDGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQV 127 Query: 121 NRRTRELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQ 180 R LL L ++D +P+ VA Q+V IA+A +V+I+DEPTS++ E E + Sbjct: 128 RDGARSLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVR 187 Query: 181 TLFKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIV 240 LF+ I +L +G I++V+H L ++ ++D ++ RDG V +AD+ LV +V Sbjct: 188 ELFRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAMV 247 Query: 241 GQELTRI---DHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSE 297 G++L + D + A + L G+ H + LQ+R+GE+LG+ GL+GSGR+E Sbjct: 248 GRDLPTVAGADAERAPPPDAPPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGRTE 307 Query: 298 FLNCIYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIAL 357 ++GL A+ G + + G+ + + P + G++L E+RK G+V S+ NI L Sbjct: 308 LARLLFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAELSVRENIVL 367 Query: 358 SAYKRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEP 417 + R W ++ ++ +LA +V+ L IK +E PV +SGGNQQKV+LA+ L TEP Sbjct: 368 ALQAR-QGWRGMSRARQDELARQLVQALGIKAADIETPVGLLSGGNQQKVMLARWLVTEP 426 Query: 418 VCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGR 475 L+ DEPTRGID AKQE+ + + G A + +S+E EL DRIAV + R Sbjct: 427 RLLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRERR 484 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: 561 Number of extensions: 26 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 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 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