Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate WP_013722122.1 ALIDE2_RS11230 pyridoxal phosphate-dependent aminotransferase
Query= curated2:O67781 (394 letters) >NCBI__GCF_000204645.1:WP_013722122.1 Length = 394 Score = 184 bits (467), Expect = 4e-51 Identities = 119/370 (32%), Positives = 188/370 (50%), Gaps = 10/370 (2%) Query: 24 AKELRAKGVDVIGFGAGEPDFDTPDFIKEACIRALREGKTKYAPSAGIPELREAIAEKLL 83 A+E+ +I GEPDF P +++A RA+R+G T+Y + G+ ELRE I+ Sbjct: 26 AREVAGTREPMIFLNIGEPDFTAPPLVRQAADRAVRDGLTQYTNALGLDELRERISGWYA 85 Query: 84 KENKVEYKPSEIVVSAGAKMVLFLIFMAILDEGDEVLLPSPYWVTYPEQIRFFGGVPVEV 143 V IVV+AGA L L +A++D GDE+L+P P + + G V V Sbjct: 86 ARFGVNVPARRIVVTAGASAALQLACLALIDAGDEILMPDPSYPCNRHFVSAADGRAVLV 145 Query: 144 PLKKEKGFQLSLEDVKEKVTERTKAIVINSPNNPTGAVYEEEELKKIAEFCVERGIFIIS 203 P E+ FQLS V+ RT+ +++ SP+NPTG +EL++I E RG + Sbjct: 146 PTTAEERFQLSAAKVEAAWGARTRGVLLASPSNPTGTSIAPDELRRIHEAVRARGGITVI 205 Query: 204 DECYEYFVYGDAKFVSPASFSDEVKNITFTVNAFSKSYSMTGWRIGYVACPEEYAKVIAS 263 DE Y Y +A + + ++V ++N+FSK ++MTGWR+G++ PE V+ Sbjct: 206 DEIYLGLSYEEAFGHTALALGEDV----ISINSFSKYFNMTGWRLGWMVVPEAMVSVVER 261 Query: 264 LNSQSVSNVTTFAQYGALEALKNPKSKDFVNEMRNAFERRRDTAVEELSKIPGMDVVKPE 323 L +T +Q+ AL + ++ R F+ RRD + L+++ V P+ Sbjct: 262 LAQNLFICASTISQHAALACFEAESIAEY-ERRRAEFKARRDFFIPALNRLGLTVPVPPD 320 Query: 324 GAFYIFPDFSAYAEKLG--GDVKLSEFLLEKAKVAVVPGSAFGAPG---FLRLSYALSEE 378 GAFY + D A +LG G + L+ +A +A+ PG FG F+R S A S Sbjct: 321 GAFYAWADCGEAARRLGVQGSWDFAFELMRRAHLAITPGRDFGTADTARFVRFSTANSMA 380 Query: 379 RLVEGIRRIK 388 +L E + R++ Sbjct: 381 QLQEAVARMQ 390 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: 333 Number of extensions: 15 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: 394 Length of database: 394 Length adjustment: 31 Effective length of query: 363 Effective length of database: 363 Effective search space: 131769 Effective search space used: 131769 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