Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate HSERO_RS08285 HSERO_RS08285 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__HerbieS:HSERO_RS08285 Length = 258 Score = 201 bits (511), Expect = 1e-56 Identities = 104/251 (41%), Positives = 159/251 (63%), Gaps = 1/251 (0%) Query: 17 SLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVL 76 ++L LS FGGL AVD + V+E + +IGPNGAGKTT+FN +S F RP GE++ Sbjct: 7 TMLEVSNLSMRFGGLLAVDGVSLAVQEREVFAIIGPNGAGKTTVFNCISGFYRPTSGEIM 66 Query: 77 FNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRV 136 +G SI + HQ+A +G VRTFQ ++ +TV+EN+L+A Q L L+ Sbjct: 67 LDGASIARQPSHQVAQQGLVRTFQNIRLFKSMTVVENLLVAQHQQVNTNLLSGLLKTPAY 126 Query: 137 QKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAG 196 +K E+ ++A L+ +GL A A AG LS G ++ +E+AR +++ P+L+LLDEPAAG Sbjct: 127 RKSEQEALQRAAYWLDQLGLTALANREAGTLSYGLQRRVEIARCMITKPRLLLLDEPAAG 186 Query: 197 VNPTLIGQICEHIVNWNRQ-GITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQS 255 +NP ++ + I R+ G+ L+IEH+M +IM + + V+ G+ + GTPEQ++S Sbjct: 187 LNPQEKQELSQLIDRLRREHGVAVLLIEHDMSLIMGISDRILVMEHGKPIVTGTPEQVRS 246 Query: 256 DPRVLEAYLGD 266 D RV++AYLG+ Sbjct: 247 DERVIKAYLGE 257 Lambda K H 0.319 0.136 0.389 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: 172 Number of extensions: 4 Number of successful extensions: 2 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: 267 Length of database: 258 Length adjustment: 25 Effective length of query: 242 Effective length of database: 233 Effective search space: 56386 Effective search space used: 56386 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