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_086508480.1 BZY95_RS02780 ABC transporter ATP-binding protein
Query= TCDB::Q7A2H0 (260 letters) >NCBI__GCF_002151265.1:WP_086508480.1 Length = 257 Score = 171 bits (434), Expect = 1e-47 Identities = 96/253 (37%), Positives = 153/253 (60%), Gaps = 15/253 (5%) Query: 11 LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70 +L GL K F G AV + ++V +G I LIGPNGAGKTT+FNLL+ F+ P +G +++ Sbjct: 6 ILETRGLTKQFRGFTAVDDVNLQVREGHIHALIGPNGAGKTTVFNLLTKFLPPTRGEILY 65 Query: 71 DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGE--NFWQVQLQPQV 128 G+PI ++ ++IA+ GMVR+FQ++ + ++ LEN+ +A Q+ G +FW+ + Sbjct: 66 RGKPITGMKANEIARMGMVRSFQISAVFAHMTALENVRVALQRPIGTSFHFWKSE----- 120 Query: 129 VVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAA 188 + L ++A+ LL+ VGL + A + G+++ LE+ L NP L+LLDEP Sbjct: 121 --RTLDHLNDRAIELLDEVGLREYADVLTVEMPYGRKRALEVATTLAMNPTLMLLDEPTQ 178 Query: 189 GVNPRLIDDICDRILTWNRQ--DGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAE 246 G+ +D+ DRI+ R+ G T L++EHN+ V+ LCD + VLA G LA+G Sbjct: 179 GMG---AEDV-DRIVALIRRVAQGRTVLMVEHNLSVVSRLCDCITVLARGAVLAEGDYQA 234 Query: 247 IQTNSQVLEAYLG 259 + + +V EAY+G Sbjct: 235 VSADPRVREAYMG 247 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: 134 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: 257 Length adjustment: 24 Effective length of query: 236 Effective length of database: 233 Effective search space: 54988 Effective search space used: 54988 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