Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Ac3H11_3369 Branched-chain amino acid aminotransferase (EC 2.6.1.42)
Query= BRENDA::P54691 (305 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3369 Length = 305 Score = 184 bits (466), Expect = 3e-51 Identities = 113/303 (37%), Positives = 170/303 (56%), Gaps = 16/303 (5%) Query: 9 YFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKSAK 68 + + + V + DAKI V TH LHYG AF G+R GT + FRL+ H DRL SAK Sbjct: 9 WMDGQMVDWRDAKIHVLTHTLHYGCGAFEGVRAYNTAN--GTAI-FRLEEHTDRLFNSAK 65 Query: 69 FLHYDI--SAEKIKEVIVDFVKKNQPDKSFYIRPLVY--SSGLGIAPRLHNLEKDFLVYG 124 L I + E++ E V++N+ + S Y+RPL + S LG++P+ + + +V Sbjct: 66 ILRMKIPFTKEEVNEAQKAVVRENKLE-SCYLRPLTWIGSQKLGVSPKGNQIH--LMVAA 122 Query: 125 LEMGDYLAADG----VSCRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFDEAI 180 G YL +G + + SS+ R + K + Y S LA EA++ G+DEA+ Sbjct: 123 WAWGAYLGEEGLKRGIRVKTSSYTRHHVNITMTQAKAVSNYTNSILANMEALDDGYDEAL 182 Query: 181 LMNSQGKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADLGIPTCQRPIDK 240 L++S G V E G N+F+++NG I TP L GITR+++ IA DLG+ Q+ I + Sbjct: 183 LLDSSGFVSEGAGENIFVIKNGVIYTPDLSAGALNGITRNTVFHIAKDLGLEIVQKRITR 242 Query: 241 SELMIADEVFLSGTAAKITPVKRIENFTLG-GDR-PITEKLRSVLTAVTENREPKYQDWV 298 E+ IADE F +GTAA++TP++ ++ LG G R PITEK++S + R Y W+ Sbjct: 243 DEVYIADEAFFTGTAAEVTPIRELDRIELGSGSRGPITEKIQSAFFDIVNGRNSNYAHWL 302 Query: 299 FKI 301 K+ Sbjct: 303 TKV 305 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: 229 Number of extensions: 12 Number of successful extensions: 4 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: 305 Length adjustment: 27 Effective length of query: 278 Effective length of database: 278 Effective search space: 77284 Effective search space used: 77284 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 Aug 03 2021. The underlying query database was built on Aug 03 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