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 Dsui_0628 Dsui_0628 ABC-type branched-chain amino acid transport system, permease component
Query= TCDB::Q8YY08 (377 letters) >FitnessBrowser__PS:Dsui_0628 Length = 358 Score = 85.1 bits (209), Expect = 3e-21 Identities = 107/363 (29%), Positives = 154/363 (42%), Gaps = 79/363 (21%) Query: 15 FALFSLGLNLQWGFTGLINFGHIAFMTLGAYTTVLLSLKGVPLFISAIVGAIFAALLGLV 74 + + +LGLN+ GF GL++ G+IAF +GAY L +L P F G + L Sbjct: 49 YIMLALGLNIVVGFAGLLDLGYIAFYAVGAY---LYALLASPHF-----GLHWPVWAILP 100 Query: 75 IGFATLRLREDYLAIVTIGTGELIRLVVNNQDLPVGDTWVSGAFGVQSYPIPLSTEPNLF 134 +G A+V G G L+ GA P L Sbjct: 101 LG-----------AVVAGGAGALL-----------------GA-------------PTLR 119 Query: 135 FRLLMIGILTLLFAVTVFSLWRWIRNAQKLQLTDATDKTSSKQEIAS--RFGVGIILGLL 192 R + I+TL F + R N L + T+ Q I+S F VG + L Sbjct: 120 LRGDYLAIVTLGFGEII----RIFMN----NLNAPVNITNGPQGISSIDPFHVGGVT--L 169 Query: 193 ATAIYISGVI--TLYNYIPKAGLMLVSLLVLAFVFWRLEYLVRSPWGRVLKAIREDEEIP 250 A + + GV +L+ Y L L+ LV+ FV RLE S GR AIREDE Sbjct: 170 AKPLSVLGVTVPSLHAYYY---LFLLLALVIIFVTIRLE---DSRIGRAWVAIREDEIAA 223 Query: 251 KAMGKNVFWYKLQSLMLGGAIAGIAGAFFAWQISAIYPDNFQPQLTFDSWIMVILGGAGN 310 KA G NV KL + +G G+AG FA + P++F + MV+LGG G+ Sbjct: 224 KACGINVRNIKLLAFSMGATFGGVAGGLFASFQGFVSPESFGLMESIMVLCMVVLGGMGH 283 Query: 311 NIGSILGAVIYFAYDAITREVLPKIIPLDEARLG-------AFRIMCIGLILMVLMIWRP 363 G ILG ++ R +PL + G + R++ GL L+ +M++RP Sbjct: 284 IPGVILGGILLTILPEAFRHA---AVPLQKYAFGKVVVDPESLRMLLFGLALIAVMLYRP 340 Query: 364 QGI 366 G+ Sbjct: 341 AGL 343 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: 441 Number of extensions: 28 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: 358 Length adjustment: 30 Effective length of query: 347 Effective length of database: 328 Effective search space: 113816 Effective search space used: 113816 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: 49 (23.5 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