Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease
Query= TCDB::P23200 (336 letters) >FitnessBrowser__BFirm:BPHYT_RS16055 Length = 335 Score = 194 bits (493), Expect = 3e-54 Identities = 115/309 (37%), Positives = 171/309 (55%), Gaps = 23/309 (7%) Query: 19 YVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQVGL 78 ++ LLV+ +++F +FLS N+ N+L Q S+ IIA+G+ +I+T G DLS G + L Sbjct: 40 FIGLLVVCIVMVFASDSFLSGANIENVLRQVSINAIIAVGMTCVILTGGIDLSVGSVMAL 99 Query: 79 AAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPFITT 138 A +AA L+ +A M + I A+G G NG +A+ + P I T Sbjct: 100 AGTLAAGLM------------VAGMNAVAALAIGIAVGLGFGAANGFFVAFAGMPPIIVT 147 Query: 139 LGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALIAVAFV- 197 L TM I G+ +Y G PI G S F G + L ++AV +V Sbjct: 148 LATMGIARGLALIY---TGGYPIDGLPDWVSFFGSGKI------LGVQAPVVIMAVIYVI 198 Query: 198 -WVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGRIGSA 256 WVL + FG+ ++AIGGN +A ++SGV V L++Y ++G+ AF ++ R+ S Sbjct: 199 AWVLLERMPFGRYVYAIGGNEQATRLSGVRVARVKLIVYTIAGLTSAFAAIVLTARLMSG 258 Query: 257 TNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPYWQYII 316 N G +ELDAIAA V+GG S SGG G++IG + G ++ V+N GL +GVNPY Q +I Sbjct: 259 QPNAGVGFELDAIAAVVMGGTSISGGRGSIIGTLIGALLLGVLNNGLNMVGVNPYVQNVI 318 Query: 317 KGAIIIFAV 325 KG II+ A+ Sbjct: 319 KGGIILLAI 327 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: 332 Number of extensions: 20 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: 335 Length adjustment: 28 Effective length of query: 308 Effective length of database: 307 Effective search space: 94556 Effective search space used: 94556 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