Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 8500738 DvMF_1481 ABC transporter related (RefSeq)
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__Miya:8500738 Length = 259 Score = 191 bits (485), Expect = 1e-53 Identities = 100/249 (40%), Positives = 152/249 (61%) Query: 17 SLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVL 76 +LL + LS +FGG+RA+D A + G+IT LIGPNGAGKTTL N ++ +RPD G V Sbjct: 2 TLLAVRDLSVAFGGIRALDAASFTAQAGAITALIGPNGAGKTTLVNCVTGMVRPDSGNVA 61 Query: 77 FNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRV 136 F+G I +A H++ G RTFQ +V +++LEN+++ L ++ V Sbjct: 62 FDGRDITGMAAHRLPRLGLARTFQHLRVFGSMSLLENVMVGLHGHVRTGMLSSMLRLPGV 121 Query: 137 QKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAG 196 ++ ERA R+ AM L+ GL +A AG L G +K L +ARAL+ +P++ILLDEP AG Sbjct: 122 RRTERAMRDAAMRALDFTGLADRADGAAGLLPYGDQKRLVLARALVGDPRMILLDEPVAG 181 Query: 197 VNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSD 256 +NP ++ I+ +G+ L+IEH+M ++M + V VL G +A+G P +++ + Sbjct: 182 LNPAETHEMGGLILALRARGVAVLLIEHDMSLVMRVSDAVVVLCSGAKIAEGAPGEVKRN 241 Query: 257 PRVLEAYLG 265 P V+ AYLG Sbjct: 242 PEVVNAYLG 250 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: 201 Number of extensions: 10 Number of successful extensions: 1 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: 259 Length adjustment: 25 Effective length of query: 242 Effective length of database: 234 Effective search space: 56628 Effective search space used: 56628 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