Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= TCDB::P23200 (336 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 166 bits (420), Expect = 8e-46 Identities = 114/325 (35%), Positives = 174/325 (53%), Gaps = 16/325 (4%) Query: 10 LTYLKEGGIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTD 69 L + ++ + LL+L+A+ + FL+ N NIL++ S+ IIA+G+ +I+ G D Sbjct: 20 LAFARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGID 79 Query: 70 LSAGRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAY 129 ++ G + A++ AA ++ ++ V AT IAL L+ IG G + G + + Sbjct: 80 VAVGSLLAFASIAAAYVVTAV-----VGDGPATWLIAL--LVSTLIGLAGGYVQGKAVTW 132 Query: 130 LNVTPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFY 189 L+V FI TLG M + G L D PISGF+ + + G + F + + Sbjct: 133 LHVPAFIVTLGGMTVWRGATLLLND---GGPISGFNDAYRWWGSGEIL---FLPVPVVIF 186 Query: 190 ALIAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLE 249 AL+A A V TR+G+ ++A+GGN EAA++SGVNV +YA+ G G L Sbjct: 187 ALVAAAG-HVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLL 245 Query: 250 AGRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVN 309 + R+GSA G YEL IA+ V+GG S +GG G V G V G ++ V++ GL + V Sbjct: 246 SARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVT 305 Query: 310 PYWQYIIKGAIIIFAVALDSLKYAR 334 Y Q ++ G II+ AVA D YAR Sbjct: 306 SYVQQVVIGLIIVAAVAFD--HYAR 328 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: 314 Number of extensions: 20 Number of successful extensions: 2 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: 332 Length adjustment: 28 Effective length of query: 308 Effective length of database: 304 Effective search space: 93632 Effective search space used: 93632 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: 49 (23.5 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