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 AO356_28510 AO356_28510 xylose transporter
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28510 Length = 518 Score = 313 bits (801), Expect = 1e-89 Identities = 191/500 (38%), Positives = 282/500 (56%), Gaps = 12/500 (2%) Query: 6 LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDA--GSI 63 LLQ + K + GV AL + +R G LCG NGAGKST + +L + G I Sbjct: 5 LLQMNGIVKTFGGVKALNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPHGTWEGEI 64 Query: 64 LLNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRR 123 + +G P++ SE AAGI +I QEL +P ++VAENI++G E G ++ A+ R Sbjct: 65 IWDGQPLKAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPGGRMNYPAMIHR 124 Query: 124 TRELLDSLEF-DVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTL 182 L+ L+ D++ + P+ + QLVEIAKA + +++I+DEP+SA+ E + L Sbjct: 125 AEALMRELKVPDMNVSLPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIEVL 184 Query: 183 FKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQ 242 IR L A+G VY+SH+L E+A + D S+ RDG + + M D+D ++ +VG+ Sbjct: 185 LDIIRDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTAMTDMDIPKIITQMVGR 244 Query: 243 ELTRI----DHKVGR---ECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGR 295 E++ + H +G E TC VDN R DIS L++GEILGI GL+G+GR Sbjct: 245 EMSNLYPTEPHDIGEVIFEARHVTCYDVDN-PRRKRVDDISFVLKRGEILGIAGLVGAGR 303 Query: 296 SEFLNCIYGLTVAD-SGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSN 354 +E ++ ++G G V L G+ + P +I AG+ +V EDRK G++ + N Sbjct: 304 TELVSALFGAYPGRYEGEVWLNGQQIDTRTPLKSIRAGLCMVPEDRKRQGIIPDLGVGQN 363 Query: 355 IALSAYKRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLS 414 I L+ S + I+A E + + R+ +KT S LP+ S+SGGNQQK VLAK L Sbjct: 364 ITLAVLDNYSKLTRIDAEAELGSIDKEIARMHLKTASPFLPITSLSGGNQQKAVLAKMLL 423 Query: 415 TEPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGG 474 T+P L+ DEPTRG+D GAK EIY L+ G + I+VSSE E+L +SDR+ V G Sbjct: 424 TKPRVLILDEPTRGVDVGAKYEIYKLMGALAAEGVSIIMVSSELAEVLGVSDRVLVIGDG 483 Query: 475 RLVTISTDTALSQEALLRLA 494 +L + L+QE +L A Sbjct: 484 QLRGDFINHELTQEQVLAAA 503 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: 592 Number of extensions: 23 Number of successful extensions: 8 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: 518 Length adjustment: 34 Effective length of query: 461 Effective length of database: 484 Effective search space: 223124 Effective search space used: 223124 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 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