Align NatE, 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 Pf6N2E2_1429 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)
Query= TCDB::Q8YT15 (247 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1429 Length = 253 Score = 160 bits (404), Expect = 3e-44 Identities = 89/243 (36%), Positives = 143/243 (58%), Gaps = 9/243 (3%) Query: 10 PLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTG-- 67 P+L+++++ Y + + ++ V+ V G++V ++G NGAGKST K L+ G Sbjct: 6 PILQIDDIEVLYEQTILAVRSVSLEVGKGQVVVLLGANGAGKSTTLKAASNLVRAERGEV 65 Query: 68 ---KITFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLK- 123 +I ++G+++ + + G+ V + + F L+VEENL GA R + L Sbjct: 66 VRGRIVYQGRDVTRSAPHTLAASGLVQVLEGRHCFAQLTVEENLLAGALARQVPRRQLLA 125 Query: 124 --DKIFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQ 181 + ++ FPRL RR+ AG SGGE+QM+A+G+ALM +P L++LDEPS L+P +V + Sbjct: 126 DLESVYGHFPRLKLRRKSLAGYTSGGEQQMIAIGRALMAKPQLVLLDEPSMGLAPQIVEE 185 Query: 182 VFEQVKQINQ-EGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELY 240 +FE V+Q+NQ +G + ++ EQN AL A GYVLESGR G ++L + + Y Sbjct: 186 IFEIVRQLNQRDGVSFLIAEQNINIALRYAHHGYVLESGRVVSEGSAEQLAARGDLQDFY 245 Query: 241 LGA 243 LGA Sbjct: 246 LGA 248 Lambda K H 0.317 0.136 0.377 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: 180 Number of extensions: 8 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 247 Length of database: 253 Length adjustment: 24 Effective length of query: 223 Effective length of database: 229 Effective search space: 51067 Effective search space used: 51067 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 46 (22.3 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