Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate AO356_20255 AO356_20255 arabinose ABC transporter permease
Query= TCDB::P23200 (336 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_20255 Length = 322 Score = 166 bits (421), Expect = 6e-46 Identities = 112/320 (35%), Positives = 169/320 (52%), Gaps = 30/320 (9%) Query: 19 YVVLLVLLAIIIF---QDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQ 75 +V+LL + I + FLS LN+ + S I A + + + DLS G Sbjct: 24 WVMLLAAIGIFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSV 83 Query: 76 VGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPF 135 + A VVAA +++ + N VF L + A+G ++GLING++IA L V Sbjct: 84 IACAGVVAAVVMR---DTNSVF---------LGVSAALAMGLIVGLINGIVIAKLRVNAL 131 Query: 136 ITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALIAVA 195 ITTL TM IV G L Y F + F F G +L + LI +A Sbjct: 132 ITTLATMQIVRG---LAYIFANGKAVGVSQESFFVFGNG-------QLFGVPVPILITIA 181 Query: 196 ----FVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAG 251 F W+L N T +G+N AIGGN EAA ++GVNV ++I+A+ G+ A G++ A Sbjct: 182 CFLFFGWLL-NYTTYGRNTMAIGGNQEAALLAGVNVDRTKIIIFAVHGLIGALAGVILAS 240 Query: 252 RIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPY 311 R+ S +G +EL I+ACV+GGVS SGG+G + V+ GV+I +I + ++ + Sbjct: 241 RMTSGQPMIGQGFELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTF 300 Query: 312 WQYIIKGAIIIFAVALDSLK 331 +QY+I+G+I++ AV +D LK Sbjct: 301 YQYVIRGSILLLAVVIDRLK 320 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: 273 Number of extensions: 16 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: 322 Length adjustment: 28 Effective length of query: 308 Effective length of database: 294 Effective search space: 90552 Effective search space used: 90552 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