Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate 7024902 Shewana3_2076 inner membrane ABC transporter permease protein YjfF (RefSeq)
Query= TCDB::P23200 (336 letters) >FitnessBrowser__ANA3:7024902 Length = 320 Score = 137 bits (345), Expect = 4e-37 Identities = 103/328 (31%), Positives = 161/328 (49%), Gaps = 39/328 (11%) Query: 21 VLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQVGLAA 80 +LL + + FQ F S ++N+L ++ +I ALG+ +I++ G DLS G + L+ Sbjct: 15 LLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSG 74 Query: 81 VVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPFITTLG 140 VV + L+ E P+ L +++ +G + G + G II + PFI TL Sbjct: 75 VVTSLLIT----------EYQWHPL-LAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLA 123 Query: 141 TMIIVYGINSLYYDFVGASPISGFDS--GFSTFAQGFVALGSFRLSYITFYALIAVAFVW 198 M + G+ + + A +D+ S G AL L +I F+ +IAV + Sbjct: 124 GMFLARGLATTLSEESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVVMHY 183 Query: 199 VLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSG----------VFYAFGGML 248 TRFG N++AIGGN +A++ G+++ + IYA+S FY F G Sbjct: 184 -----TRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYA 238 Query: 249 EAGRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIG- 307 G IG ELDAIAA V+GG +GG G V+G V GVI+ VI +T+ G Sbjct: 239 -LGAIG---------VELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGS 288 Query: 308 VNPYWQYIIKGAIIIFAVALDSLKYARK 335 ++ +W I+ G ++ F + L L RK Sbjct: 289 LSSWWTKIVIGLLLFFFILLQKLLNGRK 316 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: 310 Number of extensions: 23 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: 320 Length adjustment: 28 Effective length of query: 308 Effective length of database: 292 Effective search space: 89936 Effective search space used: 89936 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