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 6938989 Sama_3087 ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__SB2B:6938989 Length = 243 Score = 141 bits (355), Expect = 1e-38 Identities = 84/249 (33%), Positives = 137/249 (55%), Gaps = 15/249 (6%) Query: 12 LAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFD 71 L AS L KS+ + V+ + V G + GL+GPNGAGKTT F ++ ++ DKG + + Sbjct: 6 LKASNLAKSYKNRQVVKNVSLTVNTGQVVGLLGPNGAGKTTTFYMVVGLVQSDKGSIHIN 65 Query: 72 GEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVK 131 + + H A++G+ Q A +LSV +N++ +Q++ ++ Sbjct: 66 DDDLTLDPMHLRARKGIGYLPQEASIFRKLSVRDNIMAV-----------LQMRKELNTD 114 Query: 132 EEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGVN 191 E ++ EQ LLE + LSGG+R+ +E+ RAL NP+ ILLDEP AGV+ Sbjct: 115 EREEALEQ---LLEEFHITHIRDNLGMSLSGGERRRVEIARALAANPRFILLDEPFAGVD 171 Query: 192 PRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTNS 251 P + DI +I+ + G+ LI +HN+ + +C++ ++++ G +A+GTPAEI N Sbjct: 172 PISVIDI-KKIIEQLKNRGLGVLITDHNVRETLDVCEKAYIVSHGDLIAEGTPAEILDNQ 230 Query: 252 QVLEAYLGK 260 QV YLG+ Sbjct: 231 QVRAVYLGE 239 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: 129 Number of extensions: 7 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: 243 Length adjustment: 24 Effective length of query: 236 Effective length of database: 219 Effective search space: 51684 Effective search space used: 51684 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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