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 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)
Query= TCDB::P21629 (255 letters) >FitnessBrowser__Btheta:350819 Length = 463 Score = 125 bits (315), Expect = 1e-33 Identities = 79/255 (30%), Positives = 140/255 (54%), Gaps = 20/255 (7%) Query: 3 RPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLI 62 + I+EVS ++ FG A++ V L V++ + V+++GP+G GKTT+ + GF + G I Sbjct: 7 KSIIEVSHVSKFFGDKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEI 66 Query: 63 RLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPA 122 R+ G+EI P HK + V FQ LF + +N+ F L KTP Sbjct: 67 RISGKEITQTPPHK---RPVNTVFQKYALFPHLNVYDNIA----------FGLKLKKTP- 112 Query: 123 FRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAA 182 +++ + ++ A L+ V +T++ R +L+ GQQ+R+ IAR ++ P +L+LDEP A Sbjct: 113 -KQTIGKKVKAA---LKMVGMTDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLA 168 Query: 183 GLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIR 242 L+ K D++ + ++ +T + + HD + +++SD IVV+++G GTP I Sbjct: 169 ALDLKMRKDMQMELKEMHKSLGITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIY 228 Query: 243 DNP--DVIKAYLGEA 255 + P + ++GE+ Sbjct: 229 NEPINSFVADFIGES 243 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: 235 Number of extensions: 7 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: 463 Length adjustment: 29 Effective length of query: 226 Effective length of database: 434 Effective search space: 98084 Effective search space used: 98084 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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