Align NatC, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate AO356_05330 AO356_05330 leucine/isoleucine/valine transporter permease subunit
Query= TCDB::Q8YY08 (377 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_05330 Length = 418 Score = 92.8 bits (229), Expect = 2e-23 Identities = 57/164 (34%), Positives = 89/164 (54%), Gaps = 13/164 (7%) Query: 205 YNYIPKA-GLMLVSLLVLAFVFWRLEYLVRSPWGRVLKAIREDEEIPKAMGKNVFWYKLQ 263 YN I K L LV+LL+ + + L+R P GR +A+REDE +A+G N KL Sbjct: 256 YNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLS 315 Query: 264 SLMLGGAIAGIAGAFFAWQISAIYPDNFQPQLTFDSWIMVILGGAGNNIGSILGAVIYFA 323 + LG A AG AG+FFA + + P++F + +V+LGG G+ +G IL A++ Sbjct: 316 AFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMIL 375 Query: 324 YDAITREVLPKIIPLDEARLGAFRIMCIGLILMVLMIWRPQGIL 367 + RE +R++ G +++++MIWRPQG+L Sbjct: 376 LPEMMRE------------FSEYRMLMFGALMVLMMIWRPQGLL 407 Score = 82.4 bits (202), Expect = 2e-20 Identities = 54/163 (33%), Positives = 87/163 (53%), Gaps = 18/163 (11%) Query: 15 FALFSLGLNLQWGFTGLINFGHIAFMTLGAYTTVLLS-LKGVPLFISAIVGAIFAALLGL 73 + + LGLN+ G GL++ G++ F +GAY+ LLS G+ +I + + AA G Sbjct: 123 YVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATFGF 182 Query: 74 VIGFATLRLREDYLAIVTIGTGELIRLVVNN-QDLPVGDTWVS---------------GA 117 ++GF LRLR DYLAIVT+G GE+IRL + N D+ G +S A Sbjct: 183 LLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERKAA 242 Query: 118 FGVQSYPIPLSTEPNLFFRLLMIGILTLLFAV-TVFSLWRWIR 159 G+Q++ E N +++ + ++ LL A+ +F + R +R Sbjct: 243 EGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLR 285 Lambda K H 0.328 0.145 0.441 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: 491 Number of extensions: 32 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 377 Length of database: 418 Length adjustment: 31 Effective length of query: 346 Effective length of database: 387 Effective search space: 133902 Effective search space used: 133902 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: 50 (23.9 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