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 8502321 DvMF_3029 ABC transporter related (RefSeq)
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__Miya:8502321 Length = 537 Score = 259 bits (661), Expect = 2e-73 Identities = 154/481 (32%), Positives = 260/481 (54%), Gaps = 9/481 (1%) Query: 18 PAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEI 77 P ++ + GI + F V+A ++++ + PG + AL+GENGAGKSTL+ IL G R + G I Sbjct: 27 PPVVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTI 86 Query: 78 LVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSR 137 +VDG PT FAS + A+ AG+ ++Q +L D +TVAEN+ LG +P R M Sbjct: 87 VVDGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQSPDMLLRP---ARMRDE 143 Query: 138 SKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLF 197 AL +DP R+ LS+ +R V I + L ++R++I+DEPTA L+ +E D LF Sbjct: 144 VAALAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLF 203 Query: 198 RIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGR 257 + + +QGKA++FISHK E+ +AD+ + R + Q + MVGR Sbjct: 204 EAMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGR 263 Query: 258 DVENVFPKIDVAIGGPVLEIRNYSHRT--EFRDISFTLRKGEILGVYGLIGAGRSELSQS 315 D V ++D PV + + H + D+S +R+GEI+ + G+ G G+ EL ++ Sbjct: 264 D---VVLQVDAKRLTPVDTVLSVEHLSGAGLSDVSLQVRRGEIVAIAGVAGNGQKELVEA 320 Query: 316 LFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLA 375 + G+ +P +G++ + G+ R G+ Y+PE+R + + N L + Sbjct: 321 ICGLARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLTTRN 380 Query: 376 RTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVII 435 + ++ FL ++ +++ ++ P LSGGN QK+VIG+ P+VI+ Sbjct: 381 QFAKGVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEVIV 440 Query: 436 LDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFE 495 + PT+G+DI + V G + E A +++V+ +L E + ++DR+ VM G +F+ Sbjct: 441 AENPTQGLDISATEEVWGRLLE-ARSTSGVLLVTGDLNEALELADRIAVMYRGRFIDVFD 499 Query: 496 R 496 + Sbjct: 500 K 500 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: 639 Number of extensions: 38 Number of successful extensions: 8 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: 537 Length adjustment: 35 Effective length of query: 477 Effective length of database: 502 Effective search space: 239454 Effective search space used: 239454 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