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 HSERO_RS03640 HSERO_RS03640 D-ribose transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__HerbieS:HSERO_RS03640 Length = 502 Score = 386 bits (991), Expect = e-111 Identities = 212/495 (42%), Positives = 317/495 (64%), Gaps = 7/495 (1%) Query: 20 ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79 +L+MRGI + F AL ++ + + PG + AL+GENGAGKSTL+K+L+G++ P++GEIL+ Sbjct: 10 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 69 Query: 80 DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSK 139 DGRP A+ AG+ I+QE + ++VA N+F+G RTR ID M SR+ Sbjct: 70 DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 129 Query: 140 ALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRI 199 A+L L + + LSIA++ V IARAL +RIVIMDEPTAALS +E + LF + Sbjct: 130 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 189 Query: 200 VRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRDV 259 VR L+++G AI++ISH+ E+Y +AD V R V + + IV+MMVGR + Sbjct: 190 VRRLRDEGLAIIYISHRMAEVYALADRVTVL-RDGSFVGELVRDEIDSERIVQMMVGRSL 248 Query: 260 ENVFPK-----IDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQ 314 + D A V+++R + + R SF +R GE+LG GL+GAGR+EL++ Sbjct: 249 SEFYQHQRIAPADAAQLPTVMQVRALAGG-KIRPASFDVRAGEVLGFAGLVGAGRTELAR 307 Query: 315 SLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSL 374 LFG G ++LEG+ + I P+ A+RAGI YVPE+R GL L M + N T+ Sbjct: 308 LLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVA 367 Query: 375 ARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVI 434 +R +R G +R+ + +AR +RL+++ A PVG LSGGNQQKV++ +WL APKV+ Sbjct: 368 SRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVL 427 Query: 435 ILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIF 494 ILDEPT+G+DI +K+ ++ + LA++G++++++SSELPE+IG+ DRVLVM+EG+ G Sbjct: 428 ILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGEL 487 Query: 495 ERAELSPEALVRAAT 509 A ++ E ++R AT Sbjct: 488 AGAAITQENIMRLAT 502 Score = 94.4 bits (233), Expect = 9e-24 Identities = 68/244 (27%), Positives = 120/244 (49%), Gaps = 9/244 (3%) Query: 273 PVLEIR----NYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMV 328 P+L++R ++ D+ T+R GEI + G GAG+S L + L G+ P G+++ Sbjct: 9 PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 68 Query: 329 LEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAANE 388 L+G+ + + P + AGI + +E +A + + N+ + S RT R G + A Sbjct: 69 LDGRPVALRDPGASRAAGINLIYQELA---VAPNISVAANVFMGSELRT-RLGLIDHAAM 124 Query: 389 FALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSK 448 + +L A + G LS QQ+V I + L +++I+DEPT + Sbjct: 125 RSRTDAVLRQLGAGFGASDL-AGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERET 183 Query: 449 AAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAA 508 + + L EGL+II +S + E+ ++DRV V+++G G R E+ E +V+ Sbjct: 184 EQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMM 243 Query: 509 TGNA 512 G + Sbjct: 244 VGRS 247 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: 640 Number of extensions: 35 Number of successful extensions: 6 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: 502 Length adjustment: 34 Effective length of query: 478 Effective length of database: 468 Effective search space: 223704 Effective search space used: 223704 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