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 Pf6N2E2_1008 Inositol transport system ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1008 Length = 485 Score = 317 bits (813), Expect = 5e-91 Identities = 186/476 (39%), Positives = 291/476 (61%), Gaps = 18/476 (3%) Query: 51 LIGENGAGKSTLVKILTGIYRPNEGEILVDGRPTTFASAQAAI---DAGVTAIHQETVLF 107 L+GENGAGKST++KIL G + G+ ++ I + G+ I+QE L Sbjct: 1 LLGENGAGKSTILKILAGAQPADAGQGSLEFNGHVLGEHDTPIRRQEVGIITIYQEFNLI 60 Query: 108 DELTVAENIFLGHAPRTRFRTIDWQTMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVA 167 +++VAEN++LG P R +DW+ M S ++ +L L +I P ++ LS+A++ +V Sbjct: 61 ADMSVAENMYLGREP-LRHGFVDWKQMFSDAQHVLDDLGLHITPRTMVRKLSVAEQQMVE 119 Query: 168 IARALSIEARIVIMDEPTAALSRKEIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDF 227 IA+AL++ A+++IMDEPTAALS +E+D L I+ LK +G +I+++SHK +E+ D + Sbjct: 120 IAKALTMNAKLIIMDEPTAALSGREVDKLHEIITDLKAKGISIIYVSHKLNEVKACCDRY 179 Query: 228 VVFPRRSRRPVRGVSRKTPQDEIVRMMVGRDVENVFPKIDVAIGGPVLEIRNYS------ 281 +F R G D+IVR+MVGRDVE V + A G +L++++ S Sbjct: 180 TIF-RDGAYITSGDVCDVSVDDIVRLMVGRDVEFVRKPLTGAPGEVMLKVQSVSRTAAGG 238 Query: 282 ----HRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEIT-I 336 H T D+S +R GEI+G GL+GAGR+EL++ +FG G + + G++++ Sbjct: 239 GRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCDEGMIYVNGRQVSPF 298 Query: 337 HSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLARTSRRG-FLRAANEFALARKY 395 SP++ I AG+ VPE+R + L I NM+LPSL R G F+ E L + Y Sbjct: 299 KSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPSLGGLQRWGMFIDDRAETQLIQDY 358 Query: 396 AERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFI 455 +RL ++ + SV +GTLSGGNQQKV++ + +A PKV+I+DEPT+GID+G+KA VH + Sbjct: 359 QKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPTRGIDVGAKAEVHQLL 418 Query: 456 SELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALV-RAATG 510 ++A G+++I++SSELPE++ +SDR++ +EG GI E + E L+ R A G Sbjct: 419 FDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSADEATEELLMARMAQG 474 Score = 59.7 bits (143), Expect = 2e-13 Identities = 53/249 (21%), Positives = 111/249 (44%), Gaps = 29/249 (11%) Query: 38 NVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILVDGRPTT-FASAQAAIDAG 96 ++S+ + G + G GAG++ L +++ G +EG I V+GR + F S + I AG Sbjct: 249 DMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCDEGMIYVNGRQVSPFKSPREGIAAG 308 Query: 97 VTAIHQETVLFDELTVAENIFLGHAPRTRFR----------------TIDWQTMNSRSKA 140 V + ++ + FL H+ R + Q + K Sbjct: 309 VALVPED-------RKQQACFLSHSIRWNMSLPSLGGLQRWGMFIDDRAETQLIQDYQKR 361 Query: 141 LLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRIV 200 L + ++ ++ + LS + V +AR ++++ +++I+DEPT + ++ +++ Sbjct: 362 LRIKMSND---SVAIGTLSGGNQQKVILARCMALKPKVLIVDEPTRGIDVGAKAEVHQLL 418 Query: 201 RGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRDVE 260 + G A++ IS + E+ ++D V F R + VS +E++ + + V Sbjct: 419 FDMARAGVAVIVISSELPEVMAVSDRIVTF--REGQITGIVSADEATEELLMARMAQGVS 476 Query: 261 NVFPKIDVA 269 + F + VA Sbjct: 477 SSFSQQGVA 485 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: 590 Number of extensions: 37 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 512 Length of database: 485 Length adjustment: 34 Effective length of query: 478 Effective length of database: 451 Effective search space: 215578 Effective search space used: 215578 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