Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate GFF2333 PS417_11895 ABC transporter
Query= TCDB::P23200 (336 letters) >FitnessBrowser__WCS417:GFF2333 Length = 340 Score = 200 bits (508), Expect = 5e-56 Identities = 110/307 (35%), Positives = 181/307 (58%), Gaps = 13/307 (4%) Query: 30 IFQDPTFL-SLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQVGLAAVVAATLLQ 88 I +D +FL + L ++ Q S+ ++A+GV +I+T G DLS+G + L+A++AA+L Q Sbjct: 43 IVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQ 102 Query: 89 SMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPFITTLGTMIIVYGI 148 + D + VFP + +P+ + + + +G + G ING IIA + PFI TLG M+ G+ Sbjct: 103 TSDFSRAVFPSLTDLPVWIPVAMGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGL 162 Query: 149 NSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALIAVAFVWVLWNKTRFGK 208 Y + P+S ++ G + + F + + F+ IA+ + T++GK Sbjct: 163 ARYYTE---GQPVSMLSDSYTAIGHGAMPVIIFLVVAVIFH--IALRY-------TKYGK 210 Query: 209 NIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGRIGSATNNLGFMYELDA 268 +AIGGN +AA+ SG+NV +L+++Y+++G+ G++ + R + +G YELDA Sbjct: 211 YTYAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDA 270 Query: 269 IAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPYWQYIIKGAIIIFAVALD 328 IAA V+GG S +GGVG + G V G +I V+ G T++GV+ Y Q IIKG II+ AV +D Sbjct: 271 IAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVID 330 Query: 329 SLKYARK 335 + RK Sbjct: 331 QYRNKRK 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: 300 Number of extensions: 13 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