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 WP_019864731.1 METMI_RS0102945 urea ABC transporter ATP-binding protein UrtD
Query= TCDB::Q7A2H0 (260 letters) >NCBI__GCF_000384075.1:WP_019864731.1 Length = 274 Score = 144 bits (362), Expect = 3e-39 Identities = 89/252 (35%), Positives = 148/252 (58%), Gaps = 12/252 (4%) Query: 10 PLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVI 69 P+L + SF G KA+ + + + G + +IGPNGAGKTT+ ++++ +PD G V Sbjct: 32 PILYMEDVSVSFDGFKALNKLSLFIDAGELRCMIGPNGAGKTTMMDVITGKTKPDTGSVF 91 Query: 70 FDGEPIQQLQPHQ--IAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQ 127 F G+ I L+ + IAQ G+ R FQ LSV EN+ LA + T + W+ L + Sbjct: 92 F-GQTIDLLEMDEPAIAQAGICRKFQKPSVFDALSVFENLELALK--TNKGAWKT-LFFR 147 Query: 128 VVVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPA 187 + ++ ++ E ++E+VGL A+ AG LS GQ++ LE+G LM PK++L+DEP Sbjct: 148 LTGEQRDRIGE----VMETVGLTALAHSRAGILSHGQKQWLEIGMLLMQEPKVMLVDEPI 203 Query: 188 AGVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEI 247 AG+ + I+ + +L + Q + +++EH+M+ + S+ +V VL EG L +GT E+ Sbjct: 204 AGMTHQEIERTAELLL--SLQGERSLVVVEHDMEFVRSIARKVTVLHEGSVLTEGTMDEV 261 Query: 248 QTNSQVLEAYLG 259 Q + +V++ YLG Sbjct: 262 QNDPRVIQVYLG 273 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: 166 Number of extensions: 8 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: 274 Length adjustment: 25 Effective length of query: 235 Effective length of database: 249 Effective search space: 58515 Effective search space used: 58515 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 24 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