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 CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Caulo:CCNA_00903 Length = 515 Score = 317 bits (811), Expect = 8e-91 Identities = 190/495 (38%), Positives = 281/495 (56%), Gaps = 11/495 (2%) Query: 6 LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65 LL V+K++ GV AL L + G VHAL G NGAGKST + IL DAG++ Sbjct: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 Query: 66 NGAPVQ-FNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRT 124 G + + P GIA I QE P ++VAEN++LGREPRR G +VD L Sbjct: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLG-LVDWSRLRADA 121 Query: 125 RELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFK 184 + LL+ L ++ +P+ L+VA+ Q+VEIAKA + + +++IMDEPT+A+ E L Sbjct: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181 Query: 185 AIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQEL 244 I L A+ ++YVSHRL E+ + D Y++ RDG FV SG +AD++ +VR +VG+ + Sbjct: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241 Query: 245 TRIDHKVGRECAANTCLQVD-------NLSRAGEFHDISLQLRQGEILGIYGLMGSGRSE 297 + + R L+V+ LS G +S R GEI+G+ GL+G+GR++ Sbjct: 242 -EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTD 300 Query: 298 FLNCIYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIAL 357 I+G +G V + KP+ + P+ I AG+ LV EDRK G L SI N++L Sbjct: 301 LARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSL 360 Query: 358 SAYKRLSS-WSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTE 416 + K LS+ ++ R E L E ++L+IK E + +SGGNQQKV+L + ++ Sbjct: 361 PSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALT 420 Query: 417 PVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRL 476 P L+ DEPTRGID GAK E++ +L G A +V+SSE E++ +SDRI VF+ G + Sbjct: 421 PKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVI 480 Query: 477 VTISTDTALSQEALL 491 V ++E L+ Sbjct: 481 VADLDAQTATEEGLM 495 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: 610 Number of extensions: 28 Number of successful extensions: 9 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: 515 Length adjustment: 34 Effective length of query: 461 Effective length of database: 481 Effective search space: 221741 Effective search space used: 221741 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