Align NatD, 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_015739568.1 ADEG_RS08050 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8YXD0 (288 letters) >NCBI__GCF_000024605.1:WP_015739568.1 Length = 292 Score = 136 bits (343), Expect = 5e-37 Identities = 99/285 (34%), Positives = 151/285 (52%), Gaps = 11/285 (3%) Query: 7 QLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTF-FVNTFGVNIWLSM 65 QL++ G+A+GSI AL A+G L Y NFA G+FL LGAY+ V T+ V ++ Sbjct: 4 QLLLTGLAIGSIYALVALGFVLIYKASGCLNFAQGEFLLLGAYVALTLVATYKVPFLPAI 63 Query: 66 IVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWGGRNQNYNL 125 I+ + V L+ E+L+ I ++I++++GL+ +R +WG + + Sbjct: 64 ILTLAVAALVGLVVERLVLRPF--IGEPVISVIMVTLGLSALMRGIFQALWGTDTRVFP- 120 Query: 126 PITPA--LDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLDLAKVSG 183 PI P + + GV V L L LAVL + L + T G MRAVADD A G Sbjct: 121 PIFPQEPVSLGGVSVSAVYLWSLGLAVLLLLLLSLFFKFTTTGIVMRAVADDQQAALSVG 180 Query: 184 IDVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLILPLFASVILGGIGNPYGAIA 243 I V++V TW IA V ++GG + I V ++ L L + VILGG+ + GA+ Sbjct: 181 ISVKRVFGITWAIAAVVAAVGGILLSNINGVNASLA-SLGLKVLPVVILGGLESVPGAVV 239 Query: 244 AAFIIGIVQE----VSTPFLGSQYKQGVALLIMILVLLIRPKGLF 284 F+IG+++ P +G ++ V +I++LVLL+RP GLF Sbjct: 240 GGFVIGLIESFVGGYLDPLVGGGLREVVPFVILLLVLLVRPYGLF 284 Lambda K H 0.328 0.144 0.426 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: 255 Number of extensions: 18 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: 288 Length of database: 292 Length adjustment: 26 Effective length of query: 262 Effective length of database: 266 Effective search space: 69692 Effective search space used: 69692 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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