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 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 249 bits (636), Expect = 2e-70 Identities = 153/486 (31%), Positives = 255/486 (52%), Gaps = 12/486 (2%) Query: 16 DAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEG 75 D ++ + GI + F V+A ++++ + PG + AL+GENGAGKSTL+ IL+G + G Sbjct: 30 DVTPVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTG 89 Query: 76 EILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMN 135 I VDG F S + A+ AG+ ++Q +L D +TVAEN+ LG + W + Sbjct: 90 IIHVDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQSGA-------WLSPV 142 Query: 136 SRSKA---LLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKE 192 S+ L +IDP R+ DLS+ +R V I + L ++R++I+DEPTA L+ E Sbjct: 143 HMSRVVAELAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGE 202 Query: 193 IDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVR 252 + LF + + E GKAI+FISHK E+ +AD+ + R S + E+ Sbjct: 203 TEQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELAN 262 Query: 253 MMVGRDVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSEL 312 MVGR+V + G VL + + + +SF +RKGE+ + G+ G G+ EL Sbjct: 263 RMVGREVILEVAAEPLEPGDRVLHVDGLA-GDGLKGLSFEVRKGEVFAIAGVAGNGQREL 321 Query: 313 SQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLP 372 + + G+ +P G++ L G + + G+ Y+PE+R L + + N L Sbjct: 322 VECVTGLRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNFLLT 381 Query: 373 SLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPK 432 + +R FL + A AR +++ P +LSGGN QK+V+G+ P Sbjct: 382 ARGCFTRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFYRKPS 441 Query: 433 VIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAG 492 +I+ + PT+G+DI + V + E+ + +++VS +L E++ ++DRV VM G G Sbjct: 442 LIVAENPTQGLDIAATEEVWARLLEVRSHA-GVLLVSGDLNEVLALADRVAVMYRGCFIG 500 Query: 493 IFERAE 498 + +R++ Sbjct: 501 LLDRSD 506 Score = 78.6 bits (192), Expect = 5e-19 Identities = 66/217 (30%), Positives = 108/217 (49%), Gaps = 11/217 (5%) Query: 288 DISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGI 347 DI+ + G I + G GAG+S L L G +G + ++G+ + SP+DA++AGI Sbjct: 52 DITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHVDGEAVRFRSPKDALKAGI 111 Query: 348 VYVPEERGRHGLALPMPIFQNMTL-PSLARTSRRGFLRAANEFALARKYAERLDLRAAAL 406 V + L M + +N+ L S A S R E LA +Y LD+ AA Sbjct: 112 GMVYQH---FMLVDSMTVAENVLLGQSGAWLSPVHMSRVVAE--LAARYG--LDIDPAAR 164 Query: 407 SVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSII 466 V LS G +Q+V I K L +V+ILDEPT + G + + +A G +I+ Sbjct: 165 ---VCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEALHRMAENGKAIV 221 Query: 467 MVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEA 503 +S ++ E++ ++D + +++ G F +E+ EA Sbjct: 222 FISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEA 258 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: 598 Number of extensions: 38 Number of successful extensions: 7 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: 524 Length adjustment: 35 Effective length of query: 477 Effective length of database: 489 Effective search space: 233253 Effective search space used: 233253 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 Apr 09 2024. 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