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_047213081.1 PATSB16_RS05695 ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_001931675.1:WP_047213081.1 Length = 284 Score = 245 bits (625), Expect = 8e-70 Identities = 121/250 (48%), Positives = 179/250 (71%), Gaps = 1/250 (0%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 +LE+ G+ + FGGL AV+ ++ +V+ Q+V +IGPNGAGKTTVFN +TG Y+PT G IR Sbjct: 15 LLELEGVGISFGGLRAVDDLSFRVQRGQIVGLIGPNGAGKTTVFNLITGVYKPTNGHIRW 74 Query: 65 DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124 G+E+ GL KIA +G+ RTFQ +RLF +MT +EN++ +H + + GL TPA R Sbjct: 75 RGQEVTGLQPDKIAAQGIRRTFQTIRLFADMTVLENVVAGEHLQIKQRWWQGLLNTPAQR 134 Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184 R E+ ++ A L+++NL + A+ +A +L YG QRR+E+AR ++ RP +++LDEPAAGL Sbjct: 135 REEQALVDRAMEVLQQLNLVDVAHENATSLPYGVQRRVELARTLVARPELIILDEPAAGL 194 Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDN 244 N E+ L I +R + VTV+L+EHDM +VM+++D+IVVIN G +A+G P +IR+N Sbjct: 195 NEFESAGLNDTIRAIR-DAGVTVILVEHDMSVVMNVTDNIVVINFGKKIAEGKPAEIRNN 253 Query: 245 PDVIKAYLGE 254 P VI+AYLG+ Sbjct: 254 PLVIEAYLGQ 263 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: 212 Number of extensions: 10 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: 255 Length of database: 284 Length adjustment: 25 Effective length of query: 230 Effective length of database: 259 Effective search space: 59570 Effective search space used: 59570 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: 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