Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease
Query= TCDB::P23200 (336 letters) >FitnessBrowser__Koxy:BWI76_RS14865 Length = 339 Score = 198 bits (503), Expect = 2e-55 Identities = 121/315 (38%), Positives = 172/315 (54%), Gaps = 19/315 (6%) Query: 17 GIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQV 76 GI +VLLVLL ++ P F + NL NI SV I+A G+ +I+T G DLS G V Sbjct: 26 GILIVLLVLLILMSTFAPNFNRVDNLLNIARSISVNAILAAGMTFVILTSGIDLSVGSIV 85 Query: 77 GLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPFI 136 ++ VV+ V MA +P L IL +GA+ GL+NG++ AYL + PFI Sbjct: 86 AVSGVVS------------VVAAMAGIPAPLAILAGVGVGALCGLLNGVLTAYLALAPFI 133 Query: 137 TTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALIAVAF 196 TLGTM + G + Y PI F G++ + L+ Sbjct: 134 VTLGTMTFLRG---MAYTITEGQPIVSSSLSFRELGNGYL----IGIPIPVIIMLVVYLL 186 Query: 197 VWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGRIGSA 256 W + +TRFG++I+A+GGN +AA+++GV V L +Y ++GV G++ A R+ SA Sbjct: 187 AWFILERTRFGRHIYAVGGNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISA 246 Query: 257 TNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPYWQYII 316 G YELDAIAA V+GG S +GG G +IG + G II V++ GL + V + Q +I Sbjct: 247 QPTAGTGYELDAIAAVVLGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSVPFFTQLLI 306 Query: 317 KGAIIIFAVALDSLK 331 KG +II AVA+D LK Sbjct: 307 KGIVIILAVAIDGLK 321 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: 288 Number of extensions: 11 Number of successful extensions: 3 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: 339 Length adjustment: 28 Effective length of query: 308 Effective length of database: 311 Effective search space: 95788 Effective search space used: 95788 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 Apr 09 2024. 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