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 H281DRAFT_05513 H281DRAFT_05513 branched-chain amino acid transport system permease protein
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__Burk376:H281DRAFT_05513 Length = 597 Score = 169 bits (427), Expect = 2e-46 Identities = 98/250 (39%), Positives = 144/250 (57%), Gaps = 7/250 (2%) Query: 12 LAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFD 71 L + K +GG+ AV + VA G I GLIGPNGAGK+TL NL++ D GRV D Sbjct: 346 LTVESVSKQYGGVLAVSDVSFSVAAGQIHGLIGPNGAGKSTLVNLIAGNYLCDSGRVRLD 405 Query: 72 GEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGE--NFWQVQLQPQVV 129 G + L A++G+ RTFQ + + L VLEN+LL G NF + + Sbjct: 406 GADVSNLVTADRAKRGLARTFQNLQLVEALPVLENVLLGMSSADGHVANFAKWWMGRAFD 465 Query: 130 VKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAG 189 + E + +A+ +L G+ Y LS G RKL+E+ RA+ P+L+LLDEP AG Sbjct: 466 LPERR----EALEILAFFGIEHLCQAYPTELSYGHRKLVELARAIAQRPRLMLLDEPIAG 521 Query: 190 VNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQT 249 +N ++ +++ R G+T L+IEHNM+ +MSLCD + VL +G+ + GTP EI++ Sbjct: 522 LNGAEAMEVA-KVVGRLRDAGVTILLIEHNMEFVMSLCDSISVLEQGRLIGTGTPEEIRS 580 Query: 250 NSQVLEAYLG 259 + ++L AYLG Sbjct: 581 DERILRAYLG 590 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: 341 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: 597 Length adjustment: 31 Effective length of query: 229 Effective length of database: 566 Effective search space: 129614 Effective search space used: 129614 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: 50 (23.9 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