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 Synpcc7942_0513 Synpcc7942_0513 ATPase
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__SynE:Synpcc7942_0513 Length = 250 Score = 134 bits (336), Expect = 2e-36 Identities = 88/245 (35%), Positives = 132/245 (53%), Gaps = 19/245 (7%) Query: 19 KSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFDGEPIQQL 78 KS+G V + VAQG + GL+GPNGAGKTT F + + RPD+G V D + +L Sbjct: 18 KSYGKRLIVNRVSLSVAQGEVVGLLGPNGAGKTTTFYMTTGLERPDEGHVWLDETELTRL 77 Query: 79 QPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVKEEKQLQE 138 Q A+ G+ Q A L+V+EN+LL Q QTG + +E++Q E Sbjct: 78 PMTQRARLGIGYLAQEASIFRHLTVVENLLLVLQ-QTG-----------IRGREQRQRVE 125 Query: 139 QAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMT---NPKLILLDEPAAGVNPRLI 195 + LL L K A+ +SGG+R+ E+ RAL PK +LLDEP AG++P + Sbjct: 126 E---LLSEFRLEKVAHTQGIRVSGGERRRTEIARALAVGSQGPKFLLLDEPFAGIDPIAV 182 Query: 196 DDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTNSQVLE 255 ++ I+ R M LI +HN+ + + DR ++L +G+ LA G+ E+ +N V + Sbjct: 183 AEV-QEIIARLRAQQMGILITDHNVRETLKITDRAYILRDGEILAAGSAEELASNPLVRQ 241 Query: 256 AYLGK 260 YLG+ Sbjct: 242 YYLGE 246 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: 125 Number of extensions: 7 Number of successful extensions: 4 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: 250 Length adjustment: 24 Effective length of query: 236 Effective length of database: 226 Effective search space: 53336 Effective search space used: 53336 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