Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate GFF3784 Psest_3853 ABC-type branched-chain amino acid transport systems, ATPase component
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__psRCH2:GFF3784 Length = 266 Score = 170 bits (430), Expect = 3e-47 Identities = 102/262 (38%), Positives = 149/262 (56%), Gaps = 12/262 (4%) Query: 7 PAENLGSPESSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSN 66 P N G + +L A+GL K FGG AV++ D+ V+ + LIGPNGAGKTT+FNLL+ Sbjct: 10 PTGNAGRDATVMLSARGLRKEFGGFVAVNNVDLDVRHAQVHALIGPNGAGKTTVFNLLTK 69 Query: 67 FIRPDQGEVLFNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTG--- 123 F++P G + I + P ++A G VR+FQ++ V LTVL+N+ +A Q G Sbjct: 70 FLQPSAGSIRLLDHDITRTDPAKVARMGLVRSFQISAVFPHLTVLDNVRVALQRPGGLAT 129 Query: 124 EKFLPRLINFRRVQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMS 183 + +LP ++ R N E+A+ ++ESVGL K + A LS G++++LE+A L Sbjct: 130 QFWLP-------MRSLNRLN-ERALQLIESVGLADKRHELAADLSYGRKRVLEIATTLAL 181 Query: 184 NPKLILLDEPAAGVNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGR 243 PK++LLDEP AG+ + + E I Q L++EHN+ V+ LCH V VL G Sbjct: 182 EPKVLLLDEPMAGMGHEDVHVVAEIIREVATQR-AVLMVEHNLKVVADLCHQVTVLQRGE 240 Query: 244 NLADGTPEQIQSDPRVLEAYLG 265 L G + D RV AY+G Sbjct: 241 ILTSGDYRTVSQDERVRVAYMG 262 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: 167 Number of extensions: 8 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: 267 Length of database: 266 Length adjustment: 25 Effective length of query: 242 Effective length of database: 241 Effective search space: 58322 Effective search space used: 58322 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