Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate Pf1N1B4_4287 Inositol transport system permease protein
Query= TCDB::P23200 (336 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4287 Length = 340 Score = 204 bits (519), Expect = 3e-57 Identities = 118/340 (34%), Positives = 197/340 (57%), Gaps = 18/340 (5%) Query: 2 SALNKKSFLTYLKEGGIYVVLLVLLAII-----IFQDPTFL-SLLNLSNILTQSSVRIII 55 +A+ KS + E I++VL+ + + I +D +FL + L ++ Q S+ ++ Sbjct: 10 AAVPVKSRRRFPTELSIFLVLIGIGLVFEMFGWIVRDQSFLMNSQRLVLMILQVSIIGLL 69 Query: 56 ALGVAGLIVTQGTDLSAGRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAI 115 A+GV +I+T G DLS+G + L+A++AA+L Q+ D A VFP + +P+ + +++ + Sbjct: 70 AIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWIPVIVGLGV 129 Query: 116 GAVIGLINGLIIAYLNVTPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGF 175 G + G ING IIA + PFI TLG M+ G+ Y + P+S ++ G Sbjct: 130 GLLAGAINGSIIAITGIPPFIATLGMMVSARGLARYYTE---GQPVSMLSDSYTAIGHGA 186 Query: 176 VALGSFRLSYITFYALIAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIY 235 + + F + + F+ IA+ + T++GK +AIGGN +AA+ SG+NV +L+++Y Sbjct: 187 MPVIIFLVVAVIFH--IALRY-------TKYGKYTYAIGGNMQAARTSGINVKRHLVIVY 237 Query: 236 ALSGVFYAFGGMLEAGRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVII 295 +++G+ G++ + R + +G YELDAIAA V+GG S +GGVG + G V G +I Sbjct: 238 SIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALI 297 Query: 296 FTVINYGLTYIGVNPYWQYIIKGAIIIFAVALDSLKYARK 335 V+ G T++GV+ Y Q IIKG II+ AV +D + RK Sbjct: 298 LGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYRNKRK 337 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: 293 Number of extensions: 12 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: 340 Length adjustment: 28 Effective length of query: 308 Effective length of database: 312 Effective search space: 96096 Effective search space used: 96096 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