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 H281DRAFT_02375 H281DRAFT_02375 amino acid/amide ABC transporter ATP-binding protein 1, HAAT family
Query= TCDB::P21629 (255 letters) >FitnessBrowser__Burk376:H281DRAFT_02375 Length = 259 Score = 189 bits (480), Expect = 5e-53 Identities = 104/251 (41%), Positives = 158/251 (62%), Gaps = 7/251 (2%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 ILE GLT F G +AVNGVNL+V + ++IGPNGAGKTT FN LT F +PT G I Sbjct: 7 ILETRGLTREFKGFIAVNGVNLRVRRGSIHALIGPNGAGKTTCFNLLTKFLEPTAGQIVF 66 Query: 65 DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124 +GE+I +IAR+G++R+FQ +F +TA++N+ + R L T F +K+ Sbjct: 67 NGEDITNERPAQIARRGIIRSFQISAVFPHLTALQNVRIGLQRSLGTAF--HFWKS---E 121 Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184 R+ R+ + A L +V LT+FA+ L+YG++R LEIA + P +++LDEP G+ Sbjct: 122 RTLRQLDDRAMDLLTQVGLTDFADVLTVELSYGRKRALEIATTLAMEPELMLLDEPTQGM 181 Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDN 244 ++ D + ALI K+ S T+L++EH+M ++ ISD I V+ +G LA+G+ ++ N Sbjct: 182 GHEDVDRVTALIKKVSSGR--TILMVEHNMNVIAGISDTITVLQRGEVLAEGSYAEVSKN 239 Query: 245 PDVIKAYLGEA 255 P V++AY+G A Sbjct: 240 PLVMQAYMGSA 250 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: 161 Number of extensions: 8 Number of successful extensions: 3 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: 259 Length adjustment: 24 Effective length of query: 231 Effective length of database: 235 Effective search space: 54285 Effective search space used: 54285 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 17 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