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 WP_011384209.1 AMB_RS09130 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= TCDB::Q8YY08 (377 letters) >NCBI__GCF_000009985.1:WP_011384209.1 Length = 415 Score = 126 bits (317), Expect = 1e-33 Identities = 104/369 (28%), Positives = 167/369 (45%), Gaps = 72/369 (19%) Query: 5 LIFLAISTATFALFSLGLNLQWGFTGLINFGHIAFMTLGAYTTVLLSLK-GVPLFISAIV 63 L+ A + + GLN+ G GL++ G +AF +GAY+ LLS G+ ++ + Sbjct: 108 LVDKATLVLIYVMLGWGLNIVVGLAGLLDLGFVAFYAVGAYSYALLSQTFGLSFWVCLPL 167 Query: 64 GAIFAALLGLVIGFATLRLREDYLAIVTIGTGELIRLVVNN-QDLPVGDTWVSGAFGVQS 122 + AA G+V+GF LRLR DY+AIVT+G GE++R+V+ N QD+ G +S G++ Sbjct: 168 AGLLAAAFGMVLGFPVLRLRGDYIAIVTMGLGEIVRVVLQNWQDVTGGPNGIS---GIE- 223 Query: 123 YPIPLSTEPNLFFRLLMIGILTLLFAVTVFSLWRWIRNAQKLQLTDATDKTSSKQEIASR 182 P+LF L+ Q A Sbjct: 224 -------RPSLF------------------------------GLSFKMVPPEGSQTFAEF 246 Query: 183 FGVGIILGLLATAIYISGVITLYNYIPKAGLMLVSLLVLAFVFWRLEYLVRSPWGRVLKA 242 FG+ Y + ++ Y L+L L+ + R+ R P GR +A Sbjct: 247 FGLD----------YSADHRVIFLYF----LILALALLTNVITLRIR---RLPVGRAWEA 289 Query: 243 IREDEEIPKAMGKNVFWYKLQSLMLGGAIAGIAGAFFAWQISAIYPDNFQPQLTFDSWIM 302 +REDE +++G N KL + G AG AG+FFA + I P++F + + Sbjct: 290 LREDEIACRSLGINPTLVKLSAFATGAMFAGFAGSFFATRQGFISPESFTFIESAVILAI 349 Query: 303 VILGGAGNNIGSILGAVIYFAYDAITREVLPKIIPLDEARLGAFRIMCIGLILMVLMIWR 362 V+LGG G+ IG +L A++ RE L FR++ G ++++M+W+ Sbjct: 350 VVLGGMGSQIGIVLAALLLVGLPEWFRE------------LQQFRMLAFGGAMVLIMLWK 397 Query: 363 PQGILGKKE 371 P G+L +E Sbjct: 398 PAGLLSTRE 406 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: 512 Number of extensions: 34 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: 415 Length adjustment: 31 Effective length of query: 346 Effective length of database: 384 Effective search space: 132864 Effective search space used: 132864 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 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