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 H281DRAFT_03380 H281DRAFT_03380 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__Burk376:H281DRAFT_03380 Length = 515 Score = 409 bits (1050), Expect = e-118 Identities = 218/501 (43%), Positives = 323/501 (64%), Gaps = 6/501 (1%) Query: 16 DAPA---ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRP 72 D PA IL+++G+S+ FPGV ALD + + L G V A+ GENGAGKSTL+KI++G Y Sbjct: 15 DVPAPREILQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHA 74 Query: 73 NEGEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQ 132 ++G I +G+P FAS A AG+ IHQE L L+VAENI+L P+ R +D++ Sbjct: 75 DDGVICYEGKPVQFASTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPK-RGPFVDYR 133 Query: 133 TMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKE 192 T+N+ ++ L + N+ PT + LSIAQ+ +V IA+ALS++AR++IMDEPT++L+ E Sbjct: 134 TLNANAQRCLQRIGLNVSPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESE 193 Query: 193 IDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVR 252 LFRI+R L+ G AIL+ISH+ DE+ EI D V R R T +EIV Sbjct: 194 TVQLFRIIRELRADGVAILYISHRLDEMAEIVDRVTVL-RDGRHIATSDFASTTINEIVA 252 Query: 253 MMVGRDVENVFP-KIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSE 311 MVGR +++ +P + V ++ +R+ F +SF LRKGEILG GL+GAGR+E Sbjct: 253 RMVGRALDDAYPPRESVPTEQVLMRVRDLQRTDTFGPLSFDLRKGEILGFAGLMGAGRTE 312 Query: 312 LSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTL 371 +++++FG + SG + L +TI SP++AIR GI Y+ E+R + GLAL MP+ N+TL Sbjct: 313 VARAIFGAERLDSGSIQLGDTPVTIRSPREAIRHGIAYLSEDRKKDGLALSMPVAANITL 372 Query: 372 PSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAP 431 ++ S RGFLR + E A+A +Y L +R + LSGGNQQK+VI KWL Sbjct: 373 SNVRAISSRGFLRFSEETAIAERYVRELAIRTPTVKQIARNLSGGNQQKIVISKWLYRGS 432 Query: 432 KVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSA 491 +++ DEPT+GID+G+K A++ + LAA+G+ ++++SSELPE++GM+DR+ V EGL Sbjct: 433 RILFFDEPTRGIDVGAKYAIYKLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGLIT 492 Query: 492 GIFERAELSPEALVRAATGNA 512 + E + S E ++ A+G + Sbjct: 493 AVLETRQTSQEEILHYASGRS 513 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: 614 Number of extensions: 31 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: 515 Length adjustment: 35 Effective length of query: 477 Effective length of database: 480 Effective search space: 228960 Effective search space used: 228960 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