Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_106715809.1 CU100_RS07385 branched-chain amino acid aminotransferase
Query= BRENDA::F0QW25 (314 letters) >NCBI__GCF_003010935.1:WP_106715809.1 Length = 292 Score = 124 bits (311), Expect = 3e-33 Identities = 82/276 (29%), Positives = 135/276 (48%), Gaps = 12/276 (4%) Query: 28 EATIPIL---THALHYGTSIFEGIRAYWNSDNNNLYVFRARDHYVRFHDSAKIMSIKVGY 84 E +P++ +HA+ +++F+G R + + H R + SA + + Sbjct: 21 EGNVPLIGPRSHAMWLASTVFDGGRWFEGVAPD------LDRHSARVNASAIALGLMPTM 74 Query: 85 SVDELIDATVELLRANDVHEDVYIRPITFVSASTVNLDIRNLDVTTAIITVPFGHYLEPK 144 S +E+I + L+ D VYIRP+ + + D T + + ++P Sbjct: 75 STEEIIGLAKDGLKKFDGDTAVYIRPMYWGEHGGYMGVPADPDSTRFCLCLYEAPMIKPS 134 Query: 145 GIKAKVVSWLRVHNSMFPMKAKVSGIYVNSVIAIIDAKVSGFDEAILLNRDGYVAEGSGE 204 G V + R P AK +Y N+ AI++A+ GFD A++L+ G VAE Sbjct: 135 GFSLTVSPFRRPTFETMPTNAKAGCLYPNNARAILEARSRGFDNALVLDMLGNVAETGTS 194 Query: 205 NIFIIKDGILYTPPVYDSILEGITRDTVITIARDLGLTVTEKRITREELYTADEVFFTGT 264 NIF++K+G ++TP + L GITR I + D G T+ ++ ++ ADE+F TG Sbjct: 195 NIFMVKEGHIFTPAPNGTFLSGITRSRTIDVLADYGFRTTQTTLSVQDFLDADEIFSTGN 254 Query: 265 AAEVTPVVNIDGRVIGNGEPGPIALKVRSYYMDVVH 300 ++V PVV I+ RV+ +PGPIA K R Y + H Sbjct: 255 HSKVVPVVRIEDRVL---QPGPIARKARELYWEFAH 287 Lambda K H 0.321 0.139 0.409 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: 222 Number of extensions: 13 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: 314 Length of database: 292 Length adjustment: 27 Effective length of query: 287 Effective length of database: 265 Effective search space: 76055 Effective search space used: 76055 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: 48 (23.1 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
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