Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate WP_011802008.1 PNAP_RS13130 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1015 (396 letters) >NCBI__GCF_000015505.1:WP_011802008.1 Length = 463 Score = 143 bits (361), Expect = 9e-39 Identities = 111/353 (31%), Positives = 168/353 (47%), Gaps = 25/353 (7%) Query: 15 IRELFK---LLGKPGIISFAGGFPDSAMFDVEGIRAASNAALAEEPGAALQYGATEGYNP 71 +R +F+ L KPG G P +F EG+R + AE+ YG +GY P Sbjct: 100 LRRIFENRALRCKPG----CGWLPGDWLF-TEGMRRSLRNLAAEDVDLG-GYGEPKGYPP 153 Query: 72 LREQLAAFMTSKGAKDVAADNLIVTTGSQQALDLLGKTLISPGDKVIVEGPTFLATIQCF 131 LR+ + + S+ V A+ +++T GS Q LDL + L+ PGD V+V+ P + + Sbjct: 154 LRQVVRDLLASREVV-VNAEQVLLTQGSSQGLDLAARQLVRPGDAVLVDEPGYANLLFSL 212 Query: 132 RLYGAELISAPIDGNGVKTDELEKLIAEHKPKFVYLIPTFGNPSGAMLSLERRKAVLEMA 191 R GA LI AP G D LE I EH+PK + P +P+G+ L VL++A Sbjct: 213 RFLGARLIGAPRTPTGYDLDTLEARIIEHRPKVFFTQPRLQSPTGSTAVLSHLHRVLQLA 272 Query: 192 VKHNTLIVEDDPYGDLYFGDAPPPSLLNLSATVPGSRELLVHCGSLSKVLSPGLRVGWMI 251 K++ ++VE+D Y DL PSL +L + +++ S SK +SP +RVG++ Sbjct: 273 EKYDFMVVENDIYADL--DPESRPSLASLD-----QLKRVIYISSFSKTISPNIRVGYLA 325 Query: 252 APAELLGKATMCKQFSDAHTSTFAQATAAQYLKAGRMPGTLANVRKVYAERAQAMGDALR 311 A ELL K S +S F + A L GR + +R A + + L Sbjct: 326 ANPELLEDLARLKMISGLTSSEFTERLAYGALVDGRWRKHIKTLRDRLALGQRRLASLL- 384 Query: 312 KELGDAIE-FVQPQGGLFVWARLTGAGGKVADGNVLAKRAIEKGVAFVPGTPF 363 L E F +P+ G+F+WAR + + LA A E+ + PG F Sbjct: 385 --LAIGFELFCEPKAGMFLWARHPA----IQNAGELAYNAAEQDILLGPGHLF 431 Lambda K H 0.319 0.136 0.394 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: 418 Number of extensions: 28 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: 396 Length of database: 463 Length adjustment: 32 Effective length of query: 364 Effective length of database: 431 Effective search space: 156884 Effective search space used: 156884 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 (21.7 bits) S2: 51 (24.3 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