Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate 14791 b0654 glutamate and aspartate transporter subunit (NCBI)
Query= TCDB::Q8YPM8 (308 letters) >FitnessBrowser__Keio:14791 Length = 246 Score = 116 bits (290), Expect = 6e-31 Identities = 84/261 (32%), Positives = 127/261 (48%), Gaps = 22/261 (8%) Query: 45 LGIQFGFDFLKQQASFDIGETLIAYKPTDTYSLALWVGLINSLRIAFVGIILTTIVGILA 104 + I + + QQA F G T TY +W G ++ ++ I+ +VG Sbjct: 1 MSIDWNWGIFLQQAPF--GNT--------TYLGWIWSGFQVTIALSICAWIIAFLVGSFF 50 Query: 105 GIARLSDNWLVRNISLVYVEIFRNTPLLLQLLFWYFAVFLGLPRADNKISLGGFIGLSQN 164 GI R N + + +YVE+FRN PL++Q WY + LP KI + L N Sbjct: 51 GILRTVPNRFLSGLGTLYVELFRNVPLIVQFFTWYLVIPELLPE---KIGMWFKAELDPN 107 Query: 165 GLELPWFTFSPEFSALLLGLIFYTGAFIAEIVRGGIQSVSKGQWEAGRSLGLNPSLIMRL 224 + +F S L LGL +T A + E VR IQS+ +GQ A ++GL R Sbjct: 108 ---IQFFLSS----MLCLGL--FTAARVCEQVRAAIQSLPRGQKNAALAMGLTLPQAYRY 158 Query: 225 VIFPQALRVIIPPLTSQYLNLTKNSSLAIAIGYPDIYFVASTTFNQTGKAVEVMLLLMLT 284 V+ P A RVI+PP+TS+ +NL KNS++A IG D+ A + + A E + L Sbjct: 159 VLLPNAYRVIVPPMTSEMMNLVKNSAIASTIGLVDMAAQAGKLLDYSAHAWESFTAITLA 218 Query: 285 YLSLSLTISLIMNAFNRTVQI 305 Y+ ++ I L+M R V++ Sbjct: 219 YVLINAFIMLVMTLVERKVRL 239 Lambda K H 0.328 0.143 0.430 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: 186 Number of extensions: 7 Number of successful extensions: 2 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: 308 Length of database: 246 Length adjustment: 25 Effective length of query: 283 Effective length of database: 221 Effective search space: 62543 Effective search space used: 62543 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: 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