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 8502038 DvMF_2751 inner-membrane translocator (RefSeq)
Query= TCDB::Q8YXD0 (288 letters) >FitnessBrowser__Miya:8502038 Length = 301 Score = 184 bits (468), Expect = 2e-51 Identities = 107/289 (37%), Positives = 178/289 (61%), Gaps = 14/289 (4%) Query: 7 QLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNT-FGVNIWLS- 64 Q + NG+AVG I AL A+G T+ YG+L+L NFAHGD T+GAYL F + T FG++ ++S Sbjct: 6 QQLTNGLAVGGIYALIALGYTMVYGVLKLINFAHGDLFTIGAYLGFTLFTAFGLSGFVSG 65 Query: 65 ------MIVAVVGTVGVM-LLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWG 117 ++V V+G V ++ L E++ + +RS ++ + ++ ++G ++F +N ++LI+G Sbjct: 66 PGGVLLVLVMVMGLVALIGFLLERVAYRPLRS--SSRLSAVVSALGASIFFQNAVMLIYG 123 Query: 118 GRNQNYNLPITPA--LDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADD 175 + Q Y I P+ L I G+ VP +++++A ++ + AL++ Q T+IG A+RA A D Sbjct: 124 AKFQVYPNDIRPSYVLSIMGIDVPLVRIMMIAASLGLMLALYWFTQRTRIGAAIRATAID 183 Query: 176 LDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGLITA-VRPNMGWFLILPLFASVILGG 234 AK+ GIDV +VI ++I + + G M GL V MGW L F + ILGG Sbjct: 184 QGAAKLMGIDVNRVISLVFMIGPALGGVAGVMVGLYYGQVDFTMGWVYGLKAFTAAILGG 243 Query: 235 IGNPYGAIAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGL 283 IGN GA+ ++G+++ + ++ +K +A L++IL+L+IRP GL Sbjct: 244 IGNIPGAMVGGLLLGVIEALGAAYISIAWKDAIAFLVLILILIIRPTGL 292 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: 250 Number of extensions: 19 Number of successful extensions: 3 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: 301 Length adjustment: 26 Effective length of query: 262 Effective length of database: 275 Effective search space: 72050 Effective search space used: 72050 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 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