Align The high affinity sugar:H+ symporter (sugar uptake) porter of 514 aas and 12 TMSs, STP10. It transports glucose, galactose and mannose, and is therefore a hexose transporter (Rottmann et al. 2016). The 2.4 (characterized)
to candidate Echvi_2805 Echvi_2805 MFS transporter, sugar porter (SP) family
Query= TCDB::Q9LT15 (514 letters) >FitnessBrowser__Cola:Echvi_2805 Length = 448 Score = 196 bits (498), Expect = 1e-54 Identities = 146/471 (30%), Positives = 234/471 (49%), Gaps = 47/471 (9%) Query: 24 FVIMTCIVAAMGGLLFGYDLGISGGVTSMEEFLTKFFPQVESQMKKAKHDTAYCKFDNQM 83 +VI IVAA+GG LFG+D + G E F+ Q + Q+ H A Sbjct: 6 YVIFLSIVAALGGFLFGFDTAVISGA---ERFI-----QEKWQLSDWTHGMAVA------ 51 Query: 84 LQLFTSSLYLAALVASFMASVITRKHGRKVSMFIGGLAFLIGALFNAFAVNVSMLIIGRL 143 +LY ++ + + K+GRK S+ G+ + I AL +A A +V + R Sbjct: 52 -----IALY-GTVIGALFGGIPADKYGRKTSLLWIGVLYFISALGSALAPDVYSFMFFRF 105 Query: 144 LLGVGVGFANQSTPVYLSEMAPAKIRGALNIGFQMAITIGILVANLINYGTSKMAQ--HG 201 + G+GVG ++ P+Y+SE+APAK RG L +Q I GIL+A NY +MA Sbjct: 106 IGGLGVGASSVVAPMYISEIAPAKNRGVLVALYQFNIVFGILMAYFSNY-LIEMADLNES 164 Query: 202 WRVSLGLAAVPAVVMVIGSFILPDTPNSML-ERGKNEEAKQMLKKI--RGADNVDHEFQD 258 WR +G+ A+PA++ + S +P +P ++ K EEA Q+L+K G D H Sbjct: 165 WRWMMGMEAIPALIYTLLSIRVPKSPRWLIAHHNKVEEATQILRKTDPEGVDEAIH---- 220 Query: 259 LIDAVEAAKKVENPWKNIMESKYRPALIFCSAIPFFQQITGINVIMFYAPVLFKTLGFGD 318 L +K++ + + + + + I F Q++GIN I+++AP +F+ G Sbjct: 221 LAIEERNREKIKVGFAVLFKHSHLKTTLLAIMIALFNQLSGINAIIYFAPRVFEMAGIDQ 280 Query: 319 DAALMSAVITGVVNMLSTFVSIYAVDRYGRRLLFLEGGIQMFICQLLVG-SFIGARFGTS 377 +AL+S + GVVNM++T + +Y +DR GR+ L + G I I LL+ SF G G Sbjct: 281 KSALLSTIGIGVVNMIATMIGLYLIDRIGRKKLMVIGSIGYIISLLLMAYSFSG---GVI 337 Query: 378 GTGTLTPATADWILAFICVYVAGFAWSWGPLGWLVPSEICPLEIRPAGQAINVSVNMFFT 437 +G ++ F+ V++A A G + W+ SE+ P E R GQ+I + Sbjct: 338 NSG--------YLPLFVFVFIASHAVGQGSVIWVFISEVFPNETRAFGQSIGCFTHWILA 389 Query: 438 FLIGQFFLTMLCHMKFG---LFYFFASMVAIMTVFIYFLLPETKGVPIEEM 485 +I F FG +F FFA M+ + +++ +PETKG +EE+ Sbjct: 390 AVIANVF--PFFANSFGPASIFGFFAVMMGLQLLWVLTKMPETKGRSLEEI 438 Lambda K H 0.327 0.141 0.434 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: 605 Number of extensions: 33 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: 514 Length of database: 448 Length adjustment: 34 Effective length of query: 480 Effective length of database: 414 Effective search space: 198720 Effective search space used: 198720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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