Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_078430749.1 BK574_RS01735 ABC transporter permease
Query= TCDB::P23200 (336 letters) >NCBI__GCF_002019605.1:WP_078430749.1 Length = 321 Score = 145 bits (366), Expect = 1e-39 Identities = 101/324 (31%), Positives = 158/324 (48%), Gaps = 26/324 (8%) Query: 5 NKKSFLTYLKEGGIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIV 64 N KS ++ G I L +++ I +F S N NI Q S +IIALG ++ Sbjct: 11 NYKSLIS--SYGTIIAGLGIIIIFSILSPSSFASFDNFINITRQISFLVIIALGATLVMA 68 Query: 65 TQGTDLSAGRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLING 124 + DLS G L V++A L S PI +L+ +G V+G NG Sbjct: 69 VKEFDLSIGAMASLGGVLSALLAAS------------GTPIIFCLLVPIIVGFVVGFFNG 116 Query: 125 LIIAYLNVTPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLS 184 I+ V F+TTL ++ G+ ++G + F +GF LG +L+ Sbjct: 117 AIVTKFKVLSFVTTLAMGTVIGGVTFW---------LTGGATVFENIPEGFKFLGQSKLA 167 Query: 185 YITFYALIAVAFVWVLW---NKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVF 241 ++ ++I V + W ++T G+ ++AIGGN +A++VSG+N+ + +AL G+ Sbjct: 168 FLPTLSVIMFVLVIIFWYIMSQTSLGRRLYAIGGNEKASEVSGINIARYKNIAFALCGML 227 Query: 242 YAFGGMLEAGRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINY 301 AF G L A R+GSA G + L+A AA +G GV ++G + G I ++ Sbjct: 228 AAFTGALLASRLGSAHPTGGDGFFLNAYAAVFLGMTIVKNGVPNILGTLFGAAIIGIMAN 287 Query: 302 GLTYIGVNPYWQYIIKGAIIIFAV 325 GLT + V + Q II GAIII A+ Sbjct: 288 GLTILEVPSFIQNIITGAIIIIAL 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: 308 Number of extensions: 19 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: 321 Length adjustment: 28 Effective length of query: 308 Effective length of database: 293 Effective search space: 90244 Effective search space used: 90244 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 Apr 09 2024. 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