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 206141 DVU0716 branched-chain amino acid ABC transporter, ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >MicrobesOnline__882:206141 Length = 238 Score = 211 bits (537), Expect = 1e-59 Identities = 112/235 (47%), Positives = 158/235 (67%), Gaps = 3/235 (1%) Query: 12 LEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITF 71 LE+ N+H Y +V+ L G++ RV+ GE+VT++G NGAGK+T +I GL+ P G + F Sbjct: 3 LELRNLHVKY-GNVEALHGIDIRVDEGEIVTILGANGAGKTTTLMSISGLVKPSEGGVFF 61 Query: 72 KGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDK--IFAM 129 + + + L S+++V G+ P+ VF +LSV ENL +GAF D + + IF + Sbjct: 62 RDEPLHKLHSHEVVARGITQSPEGRRVFGTLSVLENLYLGAFTCRDKARVERTLGWIFEL 121 Query: 130 FPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQI 189 FPRL +RR Q AGTLSGGE+QMLA+G+ALM +P +L+LDEPS L+PILV +F+ V+ I Sbjct: 122 FPRLEERRGQLAGTLSGGEQQMLAIGRALMGDPKVLLLDEPSLGLAPILVKSIFDTVRTI 181 Query: 190 NQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLGAG 244 NQ G ++LVEQNAR AL++A RGYV+E GR + LL +P+V YLG G Sbjct: 182 NQSGVTVVLVEQNARAALKLATRGYVMEVGRVVMEDSAASLLANPEVQAAYLGGG 236 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: 177 Number of extensions: 4 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: 247 Length of database: 238 Length adjustment: 23 Effective length of query: 224 Effective length of database: 215 Effective search space: 48160 Effective search space used: 48160 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