Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_078430189.1 BK574_RS22720 branched-chain-amino-acid transaminase
Query= BRENDA::P54691 (305 letters) >NCBI__GCF_002019605.1:WP_078430189.1 Length = 301 Score = 126 bits (317), Expect = 5e-34 Identities = 100/308 (32%), Positives = 156/308 (50%), Gaps = 44/308 (14%) Query: 9 YFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKSAK 68 Y +FV +AK+SV H YG F G+R + D +F+L H +RL SAK Sbjct: 7 YLNGEFVEKHNAKVSVYDHGFLYGDGVFEGIR-VYDGN------IFQLKEHLERLYNSAK 59 Query: 69 FLHYDI--SAEKIKEVIVDFVKKNQPDKSFYIRPLVYSSGLG----------------IA 110 + I S E++ ++IV+ +K N+ + YIR LV S G+G IA Sbjct: 60 SILLTIPHSLEELTQIIVETIKINELQDA-YIR-LVVSRGVGNLGLDPASCPTPNVIVIA 117 Query: 111 PRLHNLEKDFLVYGLEMGDYLAADGVSCRISSWYRQEDRSFPLRGKI-SAAYITSALAKT 169 +L K+ GLE I + + +R L K+ S Y+ + L K Sbjct: 118 EQLSIFPKELYDKGLE-------------IVTVATRRNRPDVLSPKVKSLNYLNNILVKI 164 Query: 170 EAVESGFDEAILMNSQGKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADL 229 EA +G EA+++N++G V E + NVF+V+ +I+TP LEGITR++I+ IA DL Sbjct: 165 EASLAGVSEALMLNNEGYVAEGSADNVFIVKGNKILTPPGYIGALEGITRNAIIDIAKDL 224 Query: 230 GIPTCQRPIDKSELMIADEVFLSGTAAKITPVKRIENFTLGGDRPITEK---LRSVLTAV 286 G + P + ++ +ADEVFL+GTAA++ V +++ +G +P E L++ V Sbjct: 225 GYEVKEEPFTRHDVYVADEVFLTGTAAEVIAVVKVDGRVIGDGKPGKETNKLLQAFRQKV 284 Query: 287 TENREPKY 294 E+ E Y Sbjct: 285 VEDGEKVY 292 Lambda K H 0.320 0.138 0.406 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: 203 Number of extensions: 11 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: 305 Length of database: 301 Length adjustment: 27 Effective length of query: 278 Effective length of database: 274 Effective search space: 76172 Effective search space used: 76172 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