Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_038214117.1 Q392_RS24560 ABC transporter ATP-binding protein
Query= TCDB::Q55164 (267 letters) >NCBI__GCF_000745855.1:WP_038214117.1 Length = 257 Score = 187 bits (474), Expect = 3e-52 Identities = 110/252 (43%), Positives = 153/252 (60%), Gaps = 3/252 (1%) Query: 16 SSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEV 75 S+LL + L+ FGG+ A+D V+E +I GLIGPNGAGK++LFN +S P GE+ Sbjct: 3 SALLCVRDLTLRFGGVHALDSVSFDVEEHAICGLIGPNGAGKSSLFNCISRLYAPSSGEI 62 Query: 76 LFNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRR 135 L+ G IG LA H+IA G RTFQ + ++VL+N+ + +T L+ Sbjct: 63 LWRGQPIGTLARHRIAGLGIGRTFQNLALFGAMSVLDNVRVGSHCRTQAGLWASLLRTGA 122 Query: 136 VQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAA 195 +++EE A KAM +L VGL A A AL G +K +E+ARAL + P L+LLDEPAA Sbjct: 123 MRQEEAAVERKAMDLLRFVGLEGVAGSRADALPFGLQKRVELARALAAEPALLLLDEPAA 182 Query: 196 GVNPTLIGQICEHIVNWNRQ--GITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQI 253 G+N + + +V R+ G T LV+EH+M +M + HV VL GR LA+G+P Q+ Sbjct: 183 GLNAGELDALAA-LVRRIRETLGTTVLVVEHHMRFLMAVSDHVVVLNFGRKLAEGSPAQV 241 Query: 254 QSDPRVLEAYLG 265 Q DP V+EAYLG Sbjct: 242 QRDPAVIEAYLG 253 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: 173 Number of extensions: 5 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: 257 Length adjustment: 25 Effective length of query: 242 Effective length of database: 232 Effective search space: 56144 Effective search space used: 56144 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