Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 8500845 DvMF_1583 ABC transporter related (RefSeq)
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__Miya:8500845 Length = 240 Score = 177 bits (448), Expect = 2e-49 Identities = 103/250 (41%), Positives = 145/250 (58%), Gaps = 15/250 (6%) Query: 17 SLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVL 76 S+L + LS FGGL A+ + V++G I LIGPNGAGKTTLFN ++ F P +G+VL Sbjct: 2 SMLEIRKLSMFFGGLAALHDVNFDVRQGEILALIGPNGAGKTTLFNCVNGFYTPSEGQVL 61 Query: 77 FNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRV 136 F G I L PH++ G RTFQV K LSR++V +N+L FL Sbjct: 62 FKGQPISGLKPHKVCQMGIARTFQVVKPLSRMSVFDNVL-------ASAFLR-------- 106 Query: 137 QKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAG 196 + ++ A +L GL + L G+RK LE+ARAL + P+ +LLDE AG Sbjct: 107 NPTRKGAQDVADEVLHFTGLWDDRDQLSKGLPLGKRKRLEIARALATQPEFLLLDESFAG 166 Query: 197 VNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSD 256 +NP + + I +QGIT ++IEH+M VIM + + VL G+ +A+GTP QI +D Sbjct: 167 LNPAELDVSIDIIRGIKQQGITVMIIEHHMKVIMAISDRIVVLNFGQKIAEGTPAQISAD 226 Query: 257 PRVLEAYLGD 266 +V+EAYLG+ Sbjct: 227 RQVVEAYLGE 236 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: 177 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: 240 Length adjustment: 24 Effective length of query: 243 Effective length of database: 216 Effective search space: 52488 Effective search space used: 52488 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: 46 (22.3 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