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_2492 Synpcc7942_2492 ATPase
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__SynE:Synpcc7942_2492 Length = 237 Score = 130 bits (327), Expect = 2e-35 Identities = 77/250 (30%), Positives = 138/250 (55%), Gaps = 16/250 (6%) Query: 10 PLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVI 69 PLL S + ++G + A+ + +E+ G I LIG NGAGK+T +S + +GR+ Sbjct: 4 PLLQLSQIAVNYGAVVALTDLTLEIFPGEIVALIGANGAGKSTTLRAISRLVPLQQGRIY 63 Query: 70 FDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVV 129 +D + + + Q+ +G+ + R L+R SV N+ L A + + ++ Sbjct: 64 YDQQDLGLIPAPQLVGRGLAHCPEGRRVLARQSVRINLELGAYCR----------RDRIG 113 Query: 130 VKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAG 189 ++ + +LQ L ++ + AG LSGG++++L + RALM+ P+L+LLDEP+ G Sbjct: 114 IQTDLELQFDRF-----PRLRERQNQPAGTLSGGEQQMLAIARALMSRPRLLLLDEPSLG 168 Query: 190 VNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQT 249 + P+++ +I ++ R+ GMT L++E N + + DR +VL GQ L G A++ Sbjct: 169 LAPQIVQEIFS-VIRSLREQGMTILLVEQNATLALQTADRGYVLEAGQLLFSGPAADLLI 227 Query: 250 NSQVLEAYLG 259 + +V +AYLG Sbjct: 228 DPRVKQAYLG 237 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: 141 Number of extensions: 11 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: 237 Length adjustment: 24 Effective length of query: 236 Effective length of database: 213 Effective search space: 50268 Effective search space used: 50268 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 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