Align NatA, 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 206140 DVU0715 branched-chain amino acid ABC transporter, ATP binding protein
Query= TCDB::Q7A2H0 (260 letters) >MicrobesOnline__882:206140 Length = 255 Score = 194 bits (493), Expect = 2e-54 Identities = 106/251 (42%), Positives = 156/251 (62%), Gaps = 1/251 (0%) Query: 9 LPLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRV 68 + LL+ L K+FGG+ AV +V +GSI GLIGPNGAGKTT+FNL++ +PD G + Sbjct: 1 MSLLSLRNLTKTFGGLVAVNSVSFDVDEGSIVGLIGPNGAGKTTVFNLITGNYKPDSGDI 60 Query: 69 IFDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQV 128 FDG I+ L H+I Q G+ RTFQ R +SV+EN+L + + L Sbjct: 61 FFDGRAIKGLLTHRIVQMGIARTFQTIRLFQNMSVMENVLAGCHCRMTAGVFSAMLGTAG 120 Query: 129 VVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAA 188 +EEK+ E+A+ LE VGLA + A LS G ++LLE+ RAL T+P+ I+LDEPA Sbjct: 121 HRREEKRAIERAVRELEFVGLADQHDNLAKNLSYGNQRLLEIARALATDPRFIILDEPAG 180 Query: 189 GVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQ 248 G+N + + I R G++ L+IEH+M ++M +C+++ VL G +A+GTP+ I+ Sbjct: 181 GMNDQETAALIGTIRA-IRDRGISVLLIEHDMSLVMKVCEKLVVLEYGALIAEGTPSVIK 239 Query: 249 TNSQVLEAYLG 259 + +V+EAYLG Sbjct: 240 RDPRVIEAYLG 250 Lambda K H 0.319 0.136 0.391 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: 171 Number of extensions: 8 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: 260 Length of database: 255 Length adjustment: 24 Effective length of query: 236 Effective length of database: 231 Effective search space: 54516 Effective search space used: 54516 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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