Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_013643702.1 METBO_RS00490 branched-chain amino acid transaminase
Query= CharProtDB::CH_024500 (309 letters) >NCBI__GCF_000191585.1:WP_013643702.1 Length = 306 Score = 335 bits (860), Expect = 6e-97 Identities = 159/299 (53%), Positives = 213/299 (71%), Gaps = 1/299 (0%) Query: 9 IWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIY 68 IWFNG V W+DA +HV+SH +HYGTSVFEGIRCYD+ GP VFR ++H++RL +S KIY Sbjct: 9 IWFNGNFVDWKDANLHVLSHVVHYGTSVFEGIRCYDTKNGPAVFRLQDHIKRLINSGKIY 68 Query: 69 RFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPWG 128 R + S+++L +A D I+ N L YIRP+ F G +GV P + ++AA+ WG Sbjct: 69 RMEIPYSVEDLSQAVLDTIKINQLKECYIRPVAFRGYGELGVYP-LNCPVETVVAAWAWG 127 Query: 129 AYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALDV 188 YLG EA+E G++ SSW R AP T+P AKAG NY++S L E+ +GY E I LD Sbjct: 128 KYLGEEAIENGVNIGTSSWRRMAPGTMPNMAKAGSNYMNSQLAKMESIANGYDEAIMLDY 187 Query: 189 NGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESLY 248 G +SEG+GEN+F V DG ++TPP +SS L G+TRD++IK+A++L +EVRE+ + RE LY Sbjct: 188 QGMVSEGSGENIFVVLDGAIYTPPISSSLLSGLTRDSVIKIAQKLSLEVREENIPREMLY 247 Query: 249 LADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGWLDQV 307 +ADEVF++GTAAE+TPVRS+D I +G G G VTK+IQ+ FF L GE ED+ GWL V Sbjct: 248 IADEVFLTGTAAEVTPVRSIDKIIIGNGTRGAVTKKIQENFFSLVNGEEEDEHGWLSYV 306 Lambda K H 0.319 0.136 0.413 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: 300 Number of extensions: 13 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: 309 Length of database: 306 Length adjustment: 27 Effective length of query: 282 Effective length of database: 279 Effective search space: 78678 Effective search space used: 78678 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