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 Pf1N1B4_3216 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
Query= TCDB::Q8YY08 (377 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3216 Length = 418 Score = 145 bits (367), Expect = 2e-39 Identities = 108/364 (29%), Positives = 170/364 (46%), Gaps = 76/364 (20%) Query: 8 LAISTATFALFSLGLNLQWGFTGLINFGHIAFMTLGAYTTVLLS-LKGVPLFISAIVGAI 66 +A + + LGLN+ G GL++ G++ F +GAY+ LLS G+ +I + + Sbjct: 116 IATLVLIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYYGLSFWICLPIAGM 175 Query: 67 FAALLGLVIGFATLRLREDYLAIVTIGTGELIRLVVNNQDLPVGDTWVSGAFGVQSYPIP 126 AA G ++GF LRLR DYLAIVT+G GE+IRL + N G G G+ + P P Sbjct: 176 MAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDLTG-----GPNGISNIPKP 230 Query: 127 LSTEPNLFFRLLMIGILTLLFAVTVFSLWRWIRNAQKLQLTDATDKTSSK--QEIASRFG 184 T+F L + D+T+++ Q FG Sbjct: 231 -----------------------TLFGL--------------SFDRTAAEGLQTFHEYFG 253 Query: 185 VGIILGLLATAIYISGVITLYNYIPKA-GLMLVSLLVLAFVFWRLEYLVRSPWGRVLKAI 243 + YN I K L L+++L+ F + + L+R P GR +A+ Sbjct: 254 LE------------------YNSINKVIFLYLIAVLLSLFALFVINRLLRMPLGRAWEAL 295 Query: 244 REDEEIPKAMGKNVFWYKLQSLMLGGAIAGIAGAFFAWQISAIYPDNFQPQLTFDSWIMV 303 REDE +A+G N KL + LG AG AG+FFA + + P++F + +V Sbjct: 296 REDEIACRALGLNPTVIKLSAFTLGACFAGFAGSFFAARQGLVTPESFTFIESATILAIV 355 Query: 304 ILGGAGNNIGSILGAVIYFAYDAITREVLPKIIPLDEARLGAFRIMCIGLILMVLMIWRP 363 +LGG G+ +G +L A + + RE +R++ G +++++MIWRP Sbjct: 356 VLGGMGSQLGVVLAATVMILLPEMMRE------------FSEYRMLMFGALMVLMMIWRP 403 Query: 364 QGIL 367 QG+L Sbjct: 404 QGLL 407 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: 509 Number of extensions: 31 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: 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 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