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 Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__Cola:Echvi_1282 Length = 502 Score = 382 bits (981), Expect = e-110 Identities = 213/497 (42%), Positives = 318/497 (63%), Gaps = 9/497 (1%) Query: 20 ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79 +L ++ I++ F GVKALD+VS+ L G VTA++GENGAGKSTL+KIL+G+Y +G I Sbjct: 1 MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYY 60 Query: 80 DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSK 139 +G P F + + A + G+ IHQE L L++ ENIFLG P T +D M+ + Sbjct: 61 NGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEAA 120 Query: 140 ALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRI 199 LL L+ N+DP + L + Q+ LV IA+ALS+E++++IMDEPT+A+S +E++ LF I Sbjct: 121 QLLHRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFGI 180 Query: 200 VRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRDV 259 +R L+ +GKAI +ISHK DEL+ IAD +VV R + G ++ +++ MVGR++ Sbjct: 181 IRALRAEGKAIAYISHKLDELFAIADRYVVL-RDGKMIESGEMEGMTEEALIQKMVGREI 239 Query: 260 -------ENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSEL 312 F + +++ ++ + + +DI+F L KGE+LG++GL+GAGR+EL Sbjct: 240 VIERSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRTEL 299 Query: 313 SQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLP 372 ++LFG+ ++ L G+ PQ+A+ AG+ VPE+R + GL L M + N +L Sbjct: 300 MEALFGVLPHQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTNSSLT 359 Query: 373 SLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPK 432 + G L E LA+KY L ++A++ V LSGGNQQKVV+ KWLAT PK Sbjct: 360 VVDSILSGGLLDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWLATRPK 419 Query: 433 VIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEG-LSA 491 V++LDEPT+GIDI +K ++ I +LA EGL +I+VSSELPEI+ +SDRVLVM EG L+A Sbjct: 420 VLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAEGRLTA 479 Query: 492 GIFERAELSPEALVRAA 508 I A+ S + +++AA Sbjct: 480 NIPIDAQTSEDEILQAA 496 Score = 90.5 bits (223), Expect = 1e-22 Identities = 68/223 (30%), Positives = 103/223 (46%), Gaps = 5/223 (2%) Query: 288 DISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGI 347 D+S L+ G + + G GAG+S L + L G+ G + G + + +DA GI Sbjct: 19 DVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYYNGDPVKFQNTRDAQEKGI 78 Query: 348 VYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALS 407 + +E L + I +N+ L T G L A A + RL L Sbjct: 79 NIIHQELN---LIPYLSIRENIFLGREPETPM-GLLDVAKMHKEAAQLLHRLKLNVDP-E 133 Query: 408 VPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIM 467 PV L G QQ V I K L+ +VII+DEPT I + G I L AEG +I Sbjct: 134 TPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFGIIRALRAEGKAIAY 193 Query: 468 VSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510 +S +L E+ ++DR +V+++G E ++ EAL++ G Sbjct: 194 ISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVG 236 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: 620 Number of extensions: 33 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