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 GFF249 PGA1_c02610 putative high-affinity branched-chain amino acid transport ATP-binding protein LivG
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__Phaeo:GFF249 Length = 255 Score = 174 bits (441), Expect = 2e-48 Identities = 93/251 (37%), Positives = 146/251 (58%) Query: 9 LPLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRV 68 + LL FGG+ AV + V +G + ++GPNGAGK+T+FNL+S F +P GR+ Sbjct: 1 MSLLEIEHATLKFGGVVAVNDLSFSVEEGEVYAIVGPNGAGKSTVFNLISRFYQPHSGRL 60 Query: 69 IFDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQV 128 FDG + Q + +A G+ RTFQ +VL+N+L+ + + Sbjct: 61 SFDGRDLLQSKADAVADLGIARTFQNIELFDHATVLQNLLVGRHRHRRSTLMEELFFTPR 120 Query: 129 VVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAA 188 V +EE++ + +++ + L + GL G RK++E+GRAL + P+L+LLDEPA+ Sbjct: 121 VRREERRHRAAVEEVIDFLDLQAYRDKMIAGLPYGVRKVVELGRALASGPRLLLLDEPAS 180 Query: 189 GVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQ 248 G++ D+ I +Q G+T L++EH+M ++ S+ DRV LA+G LA+GTPAE+Q Sbjct: 181 GLSVEETRDMRWWIDDIRKQMGITVLMVEHDMGLVSSVSDRVLALADGAKLAEGTPAEVQ 240 Query: 249 TNSQVLEAYLG 259 N V+EAYLG Sbjct: 241 ANPAVIEAYLG 251 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: 174 Number of extensions: 5 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: 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