Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate Pf1N1B4_409 L-arabinose transport system permease protein (TC 3.A.1.2.2)
Query= TCDB::P23200 (336 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_409 Length = 322 Score = 164 bits (416), Expect = 2e-45 Identities = 106/315 (33%), Positives = 162/315 (51%), Gaps = 26/315 (8%) Query: 17 GIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQV 76 GI+V+ +L+ FLS LN+ + S I A + + + DLS G + Sbjct: 32 GIFVLCTLLI-------DNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVI 84 Query: 77 GLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPFI 136 A VVAA +++ D+ + L + +G ++GLING++IA L V I Sbjct: 85 ACAGVVAAVVMRDTDS------------VFLGVSAALVMGLIVGLINGIVIAKLRVNALI 132 Query: 137 TTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALIAVAF 196 TTL TM IV G L Y F + F F G + F + ++ F Sbjct: 133 TTLATMQIVRG---LAYIFANGKAVGVSQEQFFVFGNGQL----FGVPVPILITIVCFLF 185 Query: 197 VWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGRIGSA 256 L N T +G+N AIGGN EAA ++GVNV +I+A+ GV A G++ A R+ S Sbjct: 186 FGWLLNYTTYGRNTMAIGGNQEAALLAGVNVDRTKTLIFAVHGVIGALAGVILASRMTSG 245 Query: 257 TNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPYWQYII 316 +G +EL I+ACV+GGVS SGG+G + V+ GV+I +I + ++ ++QY+I Sbjct: 246 QPMIGQGFELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVI 305 Query: 317 KGAIIIFAVALDSLK 331 +G+I++ AV +D LK Sbjct: 306 RGSILLLAVVIDRLK 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: 262 Number of extensions: 14 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: 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