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 SMc03120 SMc03120 ABC transporter ATP-binding protein
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__Smeli:SMc03120 Length = 262 Score = 164 bits (415), Expect = 2e-45 Identities = 93/254 (36%), Positives = 149/254 (58%), Gaps = 11/254 (4%) Query: 8 PLPLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGR 67 P +L+A GL + FGG AV++ ++V + LIGPNGAGKTT+FNLL+ F++P G Sbjct: 12 PRVVLSARGLRRDFGGFTAVKDVDLDVHHARVHALIGPNGAGKTTVFNLLTKFLQPTHGT 71 Query: 68 VIFDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQK--QTGENFWQVQLQ 125 + GE I + P ++A+ G+VR+FQ++ L+VL+N+ +A Q+ + FW+ Sbjct: 72 ITLLGEDITRTAPDKVARMGLVRSFQISAVFPHLTVLDNVRVALQRPNRLATQFWK---- 127 Query: 126 PQVVVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDE 185 + L +A L+ SVGL K+A A LS G++++LE+ L PK++LLDE Sbjct: 128 ---SLSSLDTLNGKAEQLIRSVGLDKEANAVAADLSYGRKRVLEIATTLALEPKVLLLDE 184 Query: 186 PAAGVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPA 245 P AG+ + + + I R+ + L++EHN+ V+ +LC V VL G+ LA+G A Sbjct: 185 PMAGMGHEDVGMVAEIIREVARERAV--LMVEHNLSVVATLCHHVTVLQRGEILAEGDYA 242 Query: 246 EIQTNSQVLEAYLG 259 + + +V AY+G Sbjct: 243 TVSEDPRVRTAYMG 256 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: 133 Number of extensions: 5 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: 262 Length adjustment: 25 Effective length of query: 235 Effective length of database: 237 Effective search space: 55695 Effective search space used: 55695 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