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_011782992.1 MVAN_RS29565 phosphonate ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_000015305.1:WP_011782992.1 Length = 267 Score = 126 bits (317), Expect = 4e-34 Identities = 81/229 (35%), Positives = 121/229 (52%), Gaps = 11/229 (4%) Query: 6 LEVSGLTMRFGGLLA--VNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIR 63 +EV L +R+ G + GVNL+VE + V++IG NGAGK+T+ CL +PT G + Sbjct: 21 IEVDDLRLRYRGASTNVLAGVNLRVEHGETVALIGTNGAGKSTLLRCLVRLAEPTSGTVT 80 Query: 64 LDGEEIQGLPGHKIA--RKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTP 121 L G ++ P + R+ + FQ L +T V N++ T A +P Sbjct: 81 LAGTDVTAAPRRALRGIRRDIGFVFQRFHLIPRLTVVHNVVHGAMGRHGTR-CAWPLTSP 139 Query: 122 AFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPA 181 A R REAM L+ V L A R TL+ GQQ+R+ IAR +M RP I++ DEP Sbjct: 140 AEVR--REAMAS----LDRVGLASLAERRVDTLSGGQQQRVAIARMLMQRPTIILADEPV 193 Query: 182 AGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQG 230 A L+P + L++ + +E +VTV++ H M L MS +D +V + G Sbjct: 194 ASLDPASATAVMELLSGIAAERHVTVVMALHQMDLAMSYADRVVGLRGG 242 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: 163 Number of extensions: 8 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: 267 Length adjustment: 25 Effective length of query: 230 Effective length of database: 242 Effective search space: 55660 Effective search space used: 55660 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