Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate WP_078430887.1 BK574_RS15655 aminotransferase class V-fold PLP-dependent enzyme
Query= curated2:O67781 (394 letters) >NCBI__GCF_002019605.1:WP_078430887.1 Length = 380 Score = 275 bits (704), Expect = 1e-78 Identities = 153/358 (42%), Positives = 216/358 (60%), Gaps = 9/358 (2%) Query: 33 DVIGFGAGEPDFDTPDFIKEACIRALREGKTKYAPSAGIPELREAIAEKLLKENKVEYKP 92 DVI G PDF TP+ I A ++A EG Y+ +AGI LR+AIA K ++N + Y P Sbjct: 18 DVIDLTIGAPDFTTPENIVNANVKASLEGHHYYSSNAGIMSLRKAIAAKFERDNGISYDP 77 Query: 93 -SEIVVSAGAKMVLFLIFMAILDEGDEVLLPSPYWVTYPEQIRFFGGVPVEVPLKKEKGF 151 +EI V+ GA L L+ M +L+ GDEV+L P W Y QI GGVPV VP +E GF Sbjct: 78 ETEIDVTIGATEALGLLMMTLLNPGDEVILADPTWPNYITQILMAGGVPVRVPTYEEDGF 137 Query: 152 QLSLEDVKEKVTERTKAIVINSPNNPTGAVYEEEELKKIAEFCVERGIFIISDECYEYFV 211 L +E V+ +TE+T+AI+IN+PNNPTGA+ E++ +++ E + +++ISDE YE + Sbjct: 138 SLQVEAVEAAITEKTRAILINTPNNPTGALLEKKSVQEFVELAKKHEVYLISDEVYEKII 197 Query: 212 YGDAKFVSPASFSDEVKNITFTVNAFSKSYSMTGWRIGYVACPEEYAKVIASLNSQSVSN 271 Y + + SPAS K + TVN+FSKSY+M GWR+GYVA E + L S Sbjct: 198 YDENEHFSPASLPG-AKEVVITVNSFSKSYAMCGWRVGYVAASENVIAPLLKLQEGMASC 256 Query: 272 VTTFAQYGALEALKNPKSKDFVNEMRNAFERRRDTAVEELSKIPGMDVVKPEGAFYIFPD 331 T AQ A+ AL+ P +D V+EM ++ RRD VE L+KIPG+ V+KP GAFY+F + Sbjct: 257 ANTMAQMAAVAALEGP--QDAVDEMVKRYKERRDLMVEGLNKIPGISVIKPGGAFYLFVN 314 Query: 332 FSAYAEKLGGDVKLSEFLLEKAKVAVVPGSAFG--APGFLRLSYALSEERLVEGIRRI 387 + + + LL++ V VPGS FG G++R+ YA S+E L + + RI Sbjct: 315 IKELGK---SSQEFATELLKQTGVMTVPGSGFGEAGEGYIRICYAKSDELLQQALERI 369 Lambda K H 0.317 0.135 0.383 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: 372 Number of extensions: 21 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: 394 Length of database: 380 Length adjustment: 30 Effective length of query: 364 Effective length of database: 350 Effective search space: 127400 Effective search space used: 127400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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