Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_053544454.1 CDES_RS04460 urea ABC transporter ATP-binding protein UrtD
Query= TCDB::P21629 (255 letters) >NCBI__GCF_001277995.1:WP_053544454.1 Length = 251 Score = 157 bits (398), Expect = 2e-43 Identities = 95/250 (38%), Positives = 144/250 (57%), Gaps = 12/250 (4%) Query: 6 LEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRLD 65 L++ L + FG +AVN V+ +V V +IG NGAGKTT + ++G P G ++LD Sbjct: 3 LDIKDLKVAFGSFIAVNSVSFQVSTGDVHFLIGANGAGKTTCIDAISGL-APGQGSVKLD 61 Query: 66 GEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFRR 125 +EI G P H+IAR GV RTFQ +F+E++ ++NL +A H L G+ R Sbjct: 62 DKEILGTPVHRIARMGVGRTFQTASVFEELSVLQNLDIACGIHRPLRALFGV------RH 115 Query: 126 SEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGLN 185 ++ A LE LTE AGTL++GQ++ LEIA ++ R+LMLDEP AG++ Sbjct: 116 RIDPRIQQA---LEVTGLTELFEAQAGTLSHGQKQWLEIAMLLVQDARVLMLDEPVAGMS 172 Query: 186 PKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDNP 245 +E L+ K+ + VL++EHDM+ + + + V+N+G L +G+ + I+ NP Sbjct: 173 EEERVATGQLLKKVARDR--IVLVVEHDMEFMRRFATRVTVMNRGEILCEGSVDDIQANP 230 Query: 246 DVIKAYLGEA 255 DV YLG A Sbjct: 231 DVQSIYLGTA 240 Lambda K H 0.320 0.137 0.391 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: 154 Number of extensions: 10 Number of successful extensions: 4 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: 255 Length of database: 251 Length adjustment: 24 Effective length of query: 231 Effective length of database: 227 Effective search space: 52437 Effective search space used: 52437 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 (21.8 bits) S2: 46 (22.3 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