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 Pf6N2E2_1705 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1705 Length = 256 Score = 164 bits (415), Expect = 2e-45 Identities = 94/249 (37%), Positives = 140/249 (56%) Query: 11 LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70 LL + SF G+KA+ + V G I LIGPNGAGK++L N+L+ R D G++ F Sbjct: 4 LLEVRNVSLSFRGVKAISDLSFSVKLGEICALIGPNGAGKSSLLNILNGVYRADAGQLFF 63 Query: 71 DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVV 130 EP+ + P + A+ G+ RTFQ ++SV++N+L + F + L Sbjct: 64 AAEPLHRPHPLKAARLGIGRTFQNNALFKKMSVVDNLLTGLSRFQRTFFLEQALGLPRAR 123 Query: 131 KEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190 +E + E+A +LE + L G L+ G +K +E+GRAL+ P L+LLDEP AG+ Sbjct: 124 REARAFAERAERVLEFLELQAWRDVAVGSLAYGLQKRVELGRALIAQPTLLLLDEPMAGM 183 Query: 191 NPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTN 250 N D+ I NR G T ++IEH++ V+M L V VL G+ + DG+PAE+Q N Sbjct: 184 NAEEKQDMSRFITDINRDLGTTVILIEHDIQVVMGLSSHVVVLDYGRKVGDGSPAEVQVN 243 Query: 251 SQVLEAYLG 259 +V+ AYLG Sbjct: 244 PEVIAAYLG 252 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: 138 Number of extensions: 6 Number of successful extensions: 1 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: 256 Length adjustment: 24 Effective length of query: 236 Effective length of database: 232 Effective search space: 54752 Effective search space used: 54752 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