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 Ac3H11_4987 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
Query= TCDB::Q8YT15 (247 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4987 Length = 272 Score = 193 bits (490), Expect = 3e-54 Identities = 110/244 (45%), Positives = 151/244 (61%), Gaps = 8/244 (3%) Query: 11 LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLT-----PH 65 +LEV N+ Y K V L+G++ V G++V ++G NGAGKST K I GLL Sbjct: 9 VLEVNNIEVIYNKVVQALRGLSLAVPRGQIVALLGSNGAGKSTTLKAISGLLALEDGVVE 68 Query: 66 TGKITFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMG--AFIRNDSLQPLK 123 +G I F G+ A + Q+VR G+ +V + VF L+VEENL A P Sbjct: 69 SGSIHFNGQPTAAVAPQQLVRNGLSHVMEGRRVFEDLTVEENLVAATYALTGRSGTTPDF 128 Query: 124 DKIFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVF 183 D +++ FPRL +RR+ AG LSGGE+QMLA+G+AL+ +P L++LDEPS LSP LV +F Sbjct: 129 DLVYSYFPRLHERRKGLAGYLSGGEQQMLAIGRALIAQPQLILLDEPSLGLSPKLVEDIF 188 Query: 184 EQVKQINQE-GTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLG 242 + +IN E GT+++LVEQNA AL +A RGY++E+G+ I G + L DP V E YLG Sbjct: 189 TIIARINAERGTSMLLVEQNATVALAVAHRGYIMENGKIVIDGTAERLANDPDVREFYLG 248 Query: 243 AGKG 246 G G Sbjct: 249 MGGG 252 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: 213 Number of extensions: 11 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: 272 Length adjustment: 24 Effective length of query: 223 Effective length of database: 248 Effective search space: 55304 Effective search space used: 55304 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: 47 (22.7 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