Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate GFF2276 PGA1_c23080 ribose transport system permease protein RbsC
Query= TCDB::P23200 (336 letters) >FitnessBrowser__Phaeo:GFF2276 Length = 324 Score = 146 bits (368), Expect = 8e-40 Identities = 95/328 (28%), Positives = 164/328 (50%), Gaps = 17/328 (5%) Query: 1 MSALNKKSFLTYLKEGGIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVA 60 M+ K+ L + GI + + + +P FL+L N N++ S++ ++ALGV Sbjct: 1 MAEFTKQDIGKLLAKQGILIAFALFIIGFTIANPKFLTLDNFENVVRSSAILGVMALGVT 60 Query: 61 GLIVTQGTDLSAGRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIG 120 ++++ DLS G + + +V +D +K+ P T+ I + + +GA+IG Sbjct: 61 FVVISGNLDLSVGSMMSFSTIVV------LDLHDKLGP---TLAIPAMFAMTLCLGALIG 111 Query: 121 LINGLIIAYLNVTPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGS 180 + G YL + I TLG + ++G+ Y + F+ F QG + Sbjct: 112 FLVG----YLKLNSLIVTLGMLSAIHGLTLTYSGGKNMDIADKEGTWFAIFGQGNIL--G 165 Query: 181 FRLSYITFYALIAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGV 240 + + F AL A+ + ++ KT FG+ ++A+GGN AA SG+ + + Y +S + Sbjct: 166 IQTPILIFIALAAL--LGIILAKTPFGRKVYAVGGNGTAATFSGIRRARVVFLCYIMSAL 223 Query: 241 FYAFGGMLEAGRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVIN 300 A G+++A R + N +G EL+ +AA ++GG S GG GT+ V GV+I I Sbjct: 224 CVATAGLIQASRSMGSQNTVGQGLELEVLAAVILGGASLLGGSGTIFKTVIGVLILGFIQ 283 Query: 301 YGLTYIGVNPYWQYIIKGAIIIFAVALD 328 GL +G++ QY++ III AV LD Sbjct: 284 NGLLLVGLDFSVQYVVTWIIIILAVWLD 311 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: 244 Number of extensions: 18 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: 324 Length adjustment: 28 Effective length of query: 308 Effective length of database: 296 Effective search space: 91168 Effective search space used: 91168 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