Align RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__Caulo:CCNA_00903 Length = 515 Score = 341 bits (874), Expect = 4e-98 Identities = 193/501 (38%), Positives = 311/501 (62%), Gaps = 12/501 (2%) Query: 20 ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79 +L++ +S+ FPGV+ALD V + + G V AL+GENGAGKSTL+KIL+ + + G + Sbjct: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 Query: 80 DGRPTTFASAQAAIDA-GVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRS 138 G+ A G+ I+QE LF EL+VAEN++LG PR R +DW + + + Sbjct: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPR-RLGLVDWSRLRADA 121 Query: 139 KALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFR 198 +ALL L ++P ++ L++A++ +V IA+A+++ AR++IMDEPTAALS +E+D L Sbjct: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181 Query: 199 IVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRD 258 I+ GLK + +++++SH+ E+ + D + V R R G ++VR+MVGR Sbjct: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVM-RDGRFVASGDVADVEVADMVRLMVGRH 240 Query: 259 VENVFPKIDVAIGGPVLEIRNYSHRTE-------FRDISFTLRKGEILGVYGLIGAGRSE 311 VE K G VL++ + R +SF R GEI+G+ GL+GAGR++ Sbjct: 241 VEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTD 300 Query: 312 LSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTL 371 L++ +FG +G+++++ + + + SP+DAI+AGI+ VPE+R + G L I +N++L Sbjct: 301 LARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSL 360 Query: 372 PSLARTSRRG-FLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATA 430 PSL S G ++ E L Y ++L ++ A +G LSGGNQQKV++G+ +A Sbjct: 361 PSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALT 420 Query: 431 PKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLS 490 PKV+I+DEPT+GIDIG+KA VH +S+LA G++++++SSEL E++ +SDR++V +EG+ Sbjct: 421 PKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVI 480 Query: 491 AGIFERAELSPEALVR-AATG 510 + + E L+ ATG Sbjct: 481 VADLDAQTATEEGLMAYMATG 501 Lambda K H 0.320 0.137 0.382 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: 33 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: 512 Length of database: 515 Length adjustment: 35 Effective length of query: 477 Effective length of database: 480 Effective search space: 228960 Effective search space used: 228960 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