Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_068169777.1 HTA01S_RS09175 branched-chain amino acid transaminase
Query= BRENDA::P0AB80 (309 letters) >NCBI__GCF_001592305.1:WP_068169777.1 Length = 312 Score = 293 bits (749), Expect = 5e-84 Identities = 138/299 (46%), Positives = 205/299 (68%), Gaps = 1/299 (0%) Query: 9 IWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIY 68 IW +G+MV W DAK+HV++H LHYG FEG+R Y++ G +FR EH +RL +SAKI Sbjct: 15 IWMDGQMVDWRDAKIHVLTHTLHYGCGAFEGVRAYNAAGGTAIFRLEEHTERLFNSAKIL 74 Query: 69 RFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPWG 128 R + + +E+ EA + V+R+N L S YIRPL ++GD +GV+P G + +++AA+ WG Sbjct: 75 RMKLPFTKEEVNEAQKAVVRENKLESCYIRPLTWIGDKKLGVSPK-GNTIHLMVAAWAWG 133 Query: 129 AYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALDV 188 AYLG E L++GI SS+ R N T AKA NY +S+L E GY E + LD Sbjct: 134 AYLGEEGLKRGIRVKTSSYTRHHVNITMTQAKAVSNYTNSILANMEVTDEGYDEALLLDS 193 Query: 189 NGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESLY 248 +G++SEGAGEN+F VK+GV++TP ++ AL GITR+ + +AK+LG+E+ ++ ++R+ +Y Sbjct: 194 SGFVSEGAGENIFVVKNGVIYTPDLSAGALNGITRNTVFHIAKDLGLEIVQKRITRDEVY 253 Query: 249 LADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGWLDQV 307 +ADE F +GTAAE+TP+R +D I++G G GP+T++IQ AFF + G + WL +V Sbjct: 254 IADEAFFTGTAAEVTPIRELDRIELGAGSRGPITEKIQSAFFDIVNGRNDKYAHWLTKV 312 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: 301 Number of extensions: 9 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: 312 Length adjustment: 27 Effective length of query: 282 Effective length of database: 285 Effective search space: 80370 Effective search space used: 80370 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 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