Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_035238991.1 Q366_RS11460 branched-chain amino acid aminotransferase
Query= BRENDA::P0AB80 (309 letters) >NCBI__GCF_000745975.1:WP_035238991.1 Length = 354 Score = 134 bits (338), Expect = 2e-36 Identities = 103/318 (32%), Positives = 159/318 (50%), Gaps = 25/318 (7%) Query: 10 WFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPV-VFRHREHMQRLHDSAKIY 68 WFN + + D + S LHYG +VFEG++ Y + G + ++R R++ R++ S++ Sbjct: 41 WFNARIEPYGDFSMSPASMVLHYGQAVFEGLKAYKTKDGKIQLYRARDNFARMNRSSQGL 100 Query: 69 RFPVSQSIDELMEACRDVIRKNNL-------TSAYIRPLIFVGDVGMGVNPPAGYSTDVI 121 P ID +M+A + +I+ TS YIRP + D +GV A Y+ Sbjct: 101 CIP-EIDIDFVMDALKKLIKLEQAWIPETMGTSLYIRPTLVATDPFLGVR--ASYTYKFF 157 Query: 122 IAAFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQ 181 I P G+Y A+ L Q + V + A K GNY +SLL G +A++ GY Sbjct: 158 IILSPVGSYY-AQGL-QPVKIWVCEDHVRAVRGGVGEFKTPGNYAASLLAGEKAKKEGYN 215 Query: 182 EGIALD--VNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVRE 239 + + LD YI E N+F + + L TP S LPGITR ++I+LAK+ G++V E Sbjct: 216 QVLWLDGIELKYIEEVGAMNIFFLINDELVTPMLNGSILPGITRFSVIELAKKWGMKVSE 275 Query: 240 QVLSRESLYLA------DEVFMSGTAAEITPVRSV----DGIQVGEGRCGPVTKRIQQAF 289 + +S + + A E+F SGTAA ++PV + I +G G G V + A Sbjct: 276 RKISIDEVIAAADNGTLQEMFGSGTAAVVSPVGELRYKDRVIHIGNGEPGEVCMKFYNAV 335 Query: 290 FGLFTGETEDKWGWLDQV 307 + G ED GW++ V Sbjct: 336 TAIQYGNAEDTEGWIEVV 353 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: 274 Number of extensions: 10 Number of successful extensions: 6 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: 354 Length adjustment: 28 Effective length of query: 281 Effective length of database: 326 Effective search space: 91606 Effective search space used: 91606 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 Sep 24 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