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_013451941.1 CALNI_RS09215 ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_000183405.1:WP_013451941.1 Length = 257 Score = 214 bits (544), Expect = 2e-60 Identities = 100/250 (40%), Positives = 165/250 (66%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 +LEV + + FGG++AV GV+ KV + ++ S+IGPNGAGKT+V N +TG Y+P G I Sbjct: 4 LLEVKNIYLSFGGIMAVAGVSFKVNKGEIFSIIGPNGAGKTSVLNVITGIYKPKRGKILF 63 Query: 65 DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124 + +I LP K A+ G+VRTFQN+ LFK MT ++NL++++H ++N ++ +F Sbjct: 64 EDNDITDLPVKKRAKLGLVRTFQNLELFKGMTVLDNLMLSRHIYMNYGLISSIFYFGKAL 123 Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184 + E + E+ H ++ ++L+ + L+YG Q+R+E+AR + P++LMLDEP AG+ Sbjct: 124 KEEVKNREFVEHVIDFLDLSSVRKKHVFELSYGIQKRVELARALCLEPKLLMLDEPMAGM 183 Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDN 244 N +ET+D+ I + E +T++LIEHDM +VM +S +V ++ G + +G PE++ ++ Sbjct: 184 NTEETEDMARYIIDINEEMGITIILIEHDMNVVMDLSHRVVALDFGEKICEGKPEEVAND 243 Query: 245 PDVIKAYLGE 254 V+ AYLGE Sbjct: 244 ERVLSAYLGE 253 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: 168 Number of extensions: 3 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: 255 Length of database: 257 Length adjustment: 24 Effective length of query: 231 Effective length of database: 233 Effective search space: 53823 Effective search space used: 53823 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