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 8502321 DvMF_3029 ABC transporter related (RefSeq)
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Miya:8502321 Length = 537 Score = 252 bits (643), Expect = 3e-71 Identities = 158/495 (31%), Positives = 268/495 (54%), Gaps = 11/495 (2%) Query: 4 PLLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSI 63 P +++ + + K++ V A D L +R G + AL G NGAGKST +SIL G ++DAG+I Sbjct: 27 PPVVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTI 86 Query: 64 LLNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRR 123 +++G P F P +AL AGI M+ Q + MTVAEN+ LG+ P ++ + Sbjct: 87 VVDGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQSP---DMLLRPARMRDE 143 Query: 124 TRELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLF 183 L + VD + + LS+ + Q VEI K D +V+I+DEPT+ + E LF Sbjct: 144 VAALAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLF 203 Query: 184 KAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADI-DRDHLVRGIVGQ 242 +A+ R+ QG +V++SH+L E+ +AD+ +I R G V+ AD+ ++ L +VG+ Sbjct: 204 EAMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGR 263 Query: 243 ELT-RIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNC 301 ++ ++D K R +T L V++LS AG D+SLQ+R+GEI+ I G+ G+G+ E + Sbjct: 264 DVVLQVDAK--RLTPVDTVLSVEHLSGAG-LSDVSLQVRRGEIVAIAGVAGNGQKELVEA 320 Query: 302 IYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYK 361 I GL ++G V + G+P G++ + EDR+ ++ N L+ Sbjct: 321 ICGLARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLTTRN 380 Query: 362 RLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLL 421 + + ++ + T + +V ++ + P ++SGGN QK+V+ + +P ++ Sbjct: 381 QFAKGVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEVIV 440 Query: 422 CDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTI-- 479 + PT+G+D A +E++ L + R ++V+ + E L L+DRIAV GR + + Sbjct: 441 AENPTQGLDISATEEVWGRLLE-ARSTSGVLLVTGDLNEALELADRIAVMYRGRFIDVFD 499 Query: 480 STDTALSQEALLRLA 494 DTA Q L +A Sbjct: 500 KDDTAKVQAIGLMMA 514 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: 580 Number of extensions: 32 Number of successful extensions: 10 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: 537 Length adjustment: 35 Effective length of query: 460 Effective length of database: 502 Effective search space: 230920 Effective search space used: 230920 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