Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate YP_004144065.1 Mesci_4909 class IV aminotransferase
Query= BRENDA::F0QW25 (314 letters) >NCBI__GCF_000185905.1:YP_004144065.1 Length = 293 Score = 127 bits (320), Expect = 2e-34 Identities = 88/279 (31%), Positives = 135/279 (48%), Gaps = 18/279 (6%) Query: 28 EATIPIL---THALHYGTSIFEGIRAYWNSDNNNLYVFRARDHYVRFHDSAKIMSIKVGY 84 E + IL +HA+ GTS+F+G R + + + H R + SA + +K Sbjct: 22 EGNVAILGPRSHAMWLGTSVFDGGRWFEGVAPDLDF------HAARVNSSAIALGLKPNM 75 Query: 85 SVDELIDATVELLRANDVHEDVYIRPITFVSAST---VNLDIRNLDVTTAIITVPFGHYL 141 S D+++ T + L+ D VYIRP+ + V D + + P + Sbjct: 76 SADKIVGLTWDGLKKFDGKTAVYIRPMYWAEHGGYMGVPADPASTRFCLCLYESPM---I 132 Query: 142 EPKGIKAKVVSWLRVHNSMFPMKAKVSGIYVNSVIAIIDAKVSGFDEAILLNRDGYVAEG 201 G V + R P AK +Y N+ AI++AK+ GFD A++L+ G VAE Sbjct: 133 PATGFSVTVSPFRRPTIETMPTNAKAGCLYPNNGRAILEAKMRGFDNAMVLDMLGNVAET 192 Query: 202 SGENIFIIKDGILYTPPVYDSILEGITRDTVITIARDLGLTVTEKRITREELYTADEVFF 261 NIF++KDG ++TP + L GITR I + + G TEK ++ + ADE+F Sbjct: 193 GTSNIFLVKDGHVFTPAPNGTFLSGITRSRTIALLGEYGFRTTEKTLSVRDFLEADEIFS 252 Query: 262 TGTAAEVTPVVNIDGRVIGNGEPGPIALKVRSYYMDVVH 300 TG ++V P+ I+ R N +PGP+A K R Y D H Sbjct: 253 TGNHSKVVPITRIEDR---NLQPGPVAKKARELYWDWAH 288 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: 245 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 314 Length of database: 293 Length adjustment: 27 Effective length of query: 287 Effective length of database: 266 Effective search space: 76342 Effective search space used: 76342 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 Apr 10 2024. The underlying query database was built on Apr 09 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