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_050462656.1 AKL27_RS09910 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= TCDB::Q8YY08 (377 letters) >NCBI__GCF_001189915.1:WP_050462656.1 Length = 408 Score = 147 bits (371), Expect = 5e-40 Identities = 108/354 (30%), Positives = 174/354 (49%), Gaps = 69/354 (19%) Query: 15 FALFSLGLNLQWGFTGLINFGHIAFMTLGAYTTVLLSLK-GVPLFISAIVGAIFAALLGL 73 + + LGLN+ GF GL++ G++ F +G YT LL+ G+ + + A +AL G Sbjct: 112 YVVLGLGLNIVVGFAGLLDLGYVGFYAVGGYTYALLNQYFGLSFWECLPLAAGMSALFGF 171 Query: 74 VIGFATLRLREDYLAIVTIGTGELIRLVVNNQDLPVGDTWVSGAFGVQSYPIPLSTEPNL 133 ++GF LRLR DYLAIVT+G GE+IRL++NN G G GV P P Sbjct: 172 LLGFPVLRLRGDYLAIVTLGFGEIIRLLLNNLTSLTG-----GPDGVSGIPKP------- 219 Query: 134 FFRLLMIGILTLLFAVTVFSLWRWIRNAQKLQLTDATDKTSSKQEIASRFGVGIILGLLA 193 TVF + ++ T + + ++ ++ LGL Sbjct: 220 ----------------TVFGI--------EMARTASVEGGTTFHDM---------LGLT- 245 Query: 194 TAIYISGVITLYNYIPKAGLMLVSLLVLAFVFWRLEYLVRSPWGRVLKAIREDEEIPKAM 253 Y G + ++ Y + LL++ F ++ L+R P GR +A+R+DE +++ Sbjct: 246 ---YQGGHMVIFLYF-------LGLLLVLFTYFVTSRLIRMPMGRAWEALRDDEIACRSL 295 Query: 254 GKNVFWYKLQSLMLGGAIAGIAGAFFAWQISAIYPDNFQPQLTFDSWIMVILGGAGNNIG 313 G N KL + LG A AG+AG+FFA + + P++F + +V+LGG G+ +G Sbjct: 296 GINPTKIKLSAFTLGAAFAGLAGSFFAARQGLVNPESFTFIESALILAIVVLGGMGSQLG 355 Query: 314 SILGAVIYFAYDAITREVLPKIIPLDEARLGAFRIMCIGLILMVLMIWRPQGIL 367 IL A +L I+P +R++ GL+++++MIWRPQG+L Sbjct: 356 VILAA------------ILLTILPEVARSFAEYRMLIFGLVMVLMMIWRPQGLL 397 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: 455 Number of extensions: 24 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: 408 Length adjustment: 31 Effective length of query: 346 Effective length of database: 377 Effective search space: 130442 Effective search space used: 130442 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