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 AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21385 Length = 521 Score = 404 bits (1038), Expect = e-117 Identities = 209/497 (42%), Positives = 327/497 (65%), Gaps = 5/497 (1%) Query: 16 DAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEG 75 D P +LE+ +S+ FPGV AL +V + + PG+V AL+GENGAGKSTL+KI+ GIY+P+ G Sbjct: 23 DEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAG 82 Query: 76 EILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMN 135 E+ + G+P TF + AA+ AG+ IHQE L +++AENI++G F ID + M+ Sbjct: 83 ELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMH 142 Query: 136 SRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDD 195 + LL L N+DP ++ +LSIA+R +V IA+A+S ++ I+IMDEPT+A++ KE+ Sbjct: 143 RCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAH 202 Query: 196 LFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQD--EIVRM 253 LF I+ LK QGK I++I+HK +E++ IAD+ VF + G+ R D ++ M Sbjct: 203 LFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGA---YIGLQRADSMDGDSLISM 259 Query: 254 MVGRDVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELS 313 MVGR++ +FP + IG ++ +R+ F+ +SF L GEILG+ GL+G+GR+ ++ Sbjct: 260 MVGRELSQLFPVREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVA 319 Query: 314 QSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPS 373 +++FGIT G++ L+GQ + I P AI G + E+R GL + + +NM + Sbjct: 320 EAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAV 379 Query: 374 LARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKV 433 L + GF++ AL ++L ++ +L + TLSGGNQQK ++ +WL T P++ Sbjct: 380 LPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRI 439 Query: 434 IILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGI 493 +ILDEPT+GID+G+KA ++ IS LA+EG+++IM+SSELPE++GMSDRV+VM EG G Sbjct: 440 LILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGT 499 Query: 494 FERAELSPEALVRAATG 510 +R+E + E +++ A+G Sbjct: 500 LDRSEATQERVMQLASG 516 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: 583 Number of extensions: 34 Number of successful extensions: 7 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: 521 Length adjustment: 35 Effective length of query: 477 Effective length of database: 486 Effective search space: 231822 Effective search space used: 231822 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