Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate Ac3H11_3036 Fructose ABC transporter, permease component FrcC
Query= TCDB::P23200 (336 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3036 Length = 319 Score = 170 bits (430), Expect = 5e-47 Identities = 102/316 (32%), Positives = 159/316 (50%), Gaps = 19/316 (6%) Query: 17 GIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQV 76 G ++ L++ A Q FLS N + IL Q V +IA+G +I+T G DLS G + Sbjct: 15 GPFIALILACAFFATQSERFLSAQNFALILQQVMVVAVIAIGQTLVILTAGIDLSCGMVM 74 Query: 77 GLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVC--AIGAVIGLINGLIIAYLNVTP 134 L +V + A ++ + I C A+ + GLINGL++ + + P Sbjct: 75 ALGGIVMTKMA-------------ADYGLSAPVAIACGMAVTMLFGLINGLLVTKIKLPP 121 Query: 135 FITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALIAV 194 FI TLGT+ I + LY GA I+ +G + F LG + + L Sbjct: 122 FIVTLGTLNIAFAATQLYS---GAQTITDIPAGMTALGNTF-QLGQTAIVWGAVLMLALY 177 Query: 195 AFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGRIG 254 W +T G++++A+G +PEA +++G+ LL +Y L+G+FY +L R G Sbjct: 178 LVTWFALRETAPGRHVYAVGNSPEATRLTGIATDKVLLGVYVLAGLFYGIASLLSVARTG 237 Query: 255 SATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPYWQY 314 + N G LDAI+A V+GG S GG G ++G + G +I V GLT +GV+ +Q Sbjct: 238 AGDPNAGQTENLDAISAVVLGGTSLFGGRGVILGTLVGALIVGVFRNGLTLMGVSSVYQI 297 Query: 315 IIKGAIIIFAVALDSL 330 ++ G ++I AVA D L Sbjct: 298 LVTGILVILAVATDQL 313 Lambda K H 0.327 0.143 0.415 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: 261 Number of extensions: 16 Number of successful extensions: 4 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: 336 Length of database: 319 Length adjustment: 28 Effective length of query: 308 Effective length of database: 291 Effective search space: 89628 Effective search space used: 89628 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: 48 (23.1 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