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 RR42_RS30800 RR42_RS30800 sugar ABC transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__Cup4G11:RR42_RS30800 Length = 530 Score = 270 bits (690), Expect = 9e-77 Identities = 172/489 (35%), Positives = 276/489 (56%), Gaps = 23/489 (4%) Query: 20 ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79 IL + GI++ F + A D++S+ L G V AL+GENGAGKSTLV IL G Y + G + V Sbjct: 5 ILRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEV 64 Query: 80 DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSK 139 DG+P +AA+ AG+ +HQ L D L+V +NI LG P ++R +D + Sbjct: 65 DGQPLPPGQPRAALTAGIGMVHQHFTLADNLSVLDNIMLGTQPLWQWR-LDGHAARGKVL 123 Query: 140 ALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRI 199 AL + P R+ +LS+ +R V I +AL AR++I+DEPTA L+ E + LF Sbjct: 124 ALAERFGLAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFST 183 Query: 200 VRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRDV 259 + L +G +++FISHK DE+ ++D V R + + +T + E+ +MVGR V Sbjct: 184 LAQLIAEGLSVIFISHKLDEVLRVSDRIAVL-RGGKLVALCAAAQTTKAELAELMVGRVV 242 Query: 260 ---ENVFPKI--DVAIGG---PVLEI-----RNYSHRTEFRDISFTLRKGEILGVYGLIG 306 E V + D A G PVL + R + R R++S +R GEI+G+ G+ G Sbjct: 243 AMPERVARRSAEDGANGNAAPPVLALEHVGARAANGRALLREVSLQVRAGEIVGIAGVSG 302 Query: 307 AGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIF 366 G++ L++ G+ + G++ L G+ ++ P+ I AG+ VPE+R G+ + ++ Sbjct: 303 NGQAALAELASGMLEASEGRITLAGKPMSA-KPRAWIGAGVARVPEDRHAIGVVGDLAVW 361 Query: 367 QNMTLPSLA--RTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIG 424 +N L+ R SR G +R A AR R D+R A + VP T+SGGN QK+++G Sbjct: 362 ENAVSEQLSEPRFSRWGVIRRAAAQRFARDLVARFDVRTAGIDVPARTMSGGNMQKLILG 421 Query: 425 KWLA-----TAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMS 479 + L+ +AP++++ +PT G+DIG+ A V + + A EG +++++S +L E+ ++ Sbjct: 422 RALSVRGEGSAPRLVVASQPTWGLDIGAVAYVRARLLDAAREGAAVLLISEDLDELHALA 481 Query: 480 DRVLVMKEG 488 DR+ VM G Sbjct: 482 DRIAVMHAG 490 Score = 95.1 bits (235), Expect = 5e-24 Identities = 74/223 (33%), Positives = 112/223 (50%), Gaps = 6/223 (2%) Query: 288 DISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGI 347 DIS L++GE+L + G GAG+S L LFG +G + ++GQ + P+ A+ AGI Sbjct: 23 DISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEVDGQPLPPGQPRAALTAGI 82 Query: 348 VYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALS 407 V + LA + + N+ L + R AA LA AER L A Sbjct: 83 GMVHQH---FTLADNLSVLDNIMLGTQPLWQWRLDGHAARGKVLA--LAERFGL-AVRPQ 136 Query: 408 VPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIM 467 VG LS G +Q+V I K L +V+ILDEPT + + +++L AEGLS+I Sbjct: 137 ARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFSTLAQLIAEGLSVIF 196 Query: 468 VSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510 +S +L E++ +SDR+ V++ G + A+ + L G Sbjct: 197 ISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMVG 239 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: 657 Number of extensions: 32 Number of successful extensions: 9 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: 530 Length adjustment: 35 Effective length of query: 477 Effective length of database: 495 Effective search space: 236115 Effective search space used: 236115 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