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_RS22220 HSERO_RS22220 D-ribose transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__HerbieS:HSERO_RS22220 Length = 505 Score = 490 bits (1261), Expect = e-143 Identities = 268/508 (52%), Positives = 352/508 (69%), Gaps = 12/508 (2%) Query: 9 VTDSKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTG 68 V D T AP +L + GI + F GV AL +V + PG V AL+GENGAGKSTLVKILTG Sbjct: 4 VADDST--AP-VLSLSGIGKRFQGVVALQDVGFTVRPGEVMALLGENGAGKSTLVKILTG 60 Query: 69 IYRPNEGEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRF-R 127 I++P+EG I + GR FASAQ A+ G+TA+HQETV+F+EL+VAENI++G P R Sbjct: 61 IHQPDEGSIHLGGREVRFASAQDAMRGGITAVHQETVMFEELSVAENIWIGRQPLCGTPR 120 Query: 128 TIDWQTMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAA 187 IDW+ M ++AL LE ++ R+KDLS+AQRH V IARALS +A++VIMDEPTAA Sbjct: 121 RIDWRRMEDEARALFARLEVDLPVRARVKDLSVAQRHFVEIARALSQQAQVVIMDEPTAA 180 Query: 188 LSRKEIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQ 247 LS EI +L+RI+ L+ G A++FISHKFDE+Y +AD + V R R G + Sbjct: 181 LSHHEIGELYRIIGQLRRAGTAVIFISHKFDEIYAVADRYTVL-RDGRFIASGELADITE 239 Query: 248 DEIVRMMVGRDVENVFPKIDVAIG---GPVLEIRNYSHRTEFRDISFTLRKGEILGVYGL 304 ++V +MVGR+V VF + PVLE+++ SH +EF D+SF +R GEILG YGL Sbjct: 240 QQLVALMVGREVGQVFSRAASNTEDQTAPVLEVKHLSHPSEFDDVSFAVRPGEILGFYGL 299 Query: 305 IGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMP 364 +GAGRSE+ +LFG++ G + ++G+E+ + SP AI G+ YVPE+R R G L +P Sbjct: 300 VGAGRSEVMHALFGLSPEAQGAVWIDGREVKLCSPAQAIAHGLAYVPEDRQRQGALLSLP 359 Query: 365 IFQNMTLPSLARTSRRGFLRA--ANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVV 422 IFQN+TLP L FLR E +AR+ E+L+L+A+ V LSGGNQQKVV Sbjct: 360 IFQNITLPVLPGIGF--FLRRHRRREIDIARRLCEQLELKASHFHQHVAQLSGGNQQKVV 417 Query: 423 IGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRV 482 + KWLAT P+V+ILDEPTKGIDIGSKAAVH FI EL A+GL++I+VSSELPE++GMSDR+ Sbjct: 418 LAKWLATQPRVLILDEPTKGIDIGSKAAVHRFIGELVAQGLAVILVSSELPEVMGMSDRI 477 Query: 483 LVMKEGLSAGIFERAELSPEALVRAATG 510 +VM +G +F RAE S EAL AA+G Sbjct: 478 VVMHQGRVQQVFSRAEASAEALAAAASG 505 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: 693 Number of extensions: 26 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: 512 Length of database: 505 Length adjustment: 34 Effective length of query: 478 Effective length of database: 471 Effective search space: 225138 Effective search space used: 225138 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