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_104486936.1 UN63_RS11730 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= TCDB::Q8YY08 (377 letters) >NCBI__GCF_002936955.1:WP_104486936.1 Length = 413 Score = 100 bits (250), Expect = 6e-26 Identities = 98/371 (26%), Positives = 156/371 (42%), Gaps = 93/371 (25%) Query: 8 LAISTATFALFSLGLNLQWGFTGLINFGHIAFMTLGAYTTVLLSLKGVPLFISAIVGAIF 67 LA T + + LGLN+ G GL++ G++AF VGA Sbjct: 114 LATLTLIYVMLGLGLNVVVGLAGLLDLGYVAFYA---------------------VGAYS 152 Query: 68 AALLGLVIGFATLRLREDYLAIVTIGTGELIRLVVNNQDLPVGDTWVSGAFGVQSYPIPL 127 ALL +GF D+ + I G ++ FG L Sbjct: 153 YALLNAYLGF-------DFWTCLLISGG------------------MAALFGF------L 181 Query: 128 STEPNLFFRLLMIGILTLLFAVTVFSLWRWIRNAQKLQLTDATDKTSSKQEIA-----SR 182 P L R + I+TL F + ++ L + T+ T IA + Sbjct: 182 LGFPVLRLRGDYLAIVTLGFGEII-----------RILLNNMTELTGGPNGIAGIPKPTL 230 Query: 183 FGVGI------ILGLLATAIYISGVITLYNYIPKAGLMLVSLLVLAFVFWRLEYLVRSPW 236 FG+ Y SG ++ Y L++LL++ F + + L+R P Sbjct: 231 FGLEFERRGDNTFHQFFDIAYNSGHKVIFLY-------LLALLLVVFTIFIINRLLRMPL 283 Query: 237 GRVLKAIREDEEIPKAMGKNVFWYKLQSLMLGGAIAGIAGAFFAWQISAIYPDNFQPQLT 296 GR +A+REDE +++G N KL + +G A AG AG+FFA + I P++F + Sbjct: 284 GRAWEALREDEIACRSLGLNPTLIKLSAFTIGAAFAGFAGSFFAARQGFISPESFVFIES 343 Query: 297 FDSWIMVILGGAGNNIGSILGAVIYFAYDAITREVLPKIIPLDEARLGAFRIMCIGLILM 356 +V+LGG G+ IG +L A++ +TRE +R++ GL+++ Sbjct: 344 AIILAIVVLGGMGSQIGVVLAAIVMTILPELTRE------------FNEYRMLLFGLLMV 391 Query: 357 VLMIWRPQGIL 367 ++MIWRPQG+L Sbjct: 392 LMMIWRPQGLL 402 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: 497 Number of extensions: 33 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 377 Length of database: 413 Length adjustment: 31 Effective length of query: 346 Effective length of database: 382 Effective search space: 132172 Effective search space used: 132172 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 24 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