Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate WP_092344251.1 BLU87_RS01970 pyridoxal phosphate-dependent aminotransferase
Query= curated2:O67781 (394 letters) >NCBI__GCF_900107645.1:WP_092344251.1 Length = 384 Score = 221 bits (562), Expect = 4e-62 Identities = 134/390 (34%), Positives = 211/390 (54%), Gaps = 18/390 (4%) Query: 1 MRKGLASRVSHLKPSPTLTITAKAKELRAKGVDVIGFGAGEPDFDTPDFIKEACIRALRE 60 M+ ++ R ++P + + +AKEL G DVI GEPDF+TP I A +AL E Sbjct: 1 MQIPISKRAKLVEPFLAMELMERAKELETAGQDVIYLCLGEPDFNTPAAILAATGQALAE 60 Query: 61 GKTKYAPSAGIPELREAIAEKLLKENKVEYKPSEIVVSAGAKMVLFLIFMAILDEGDEVL 120 G T Y S G+ ELR+ I L V+ P +++VS+G ++ L+F +LD+GDE++ Sbjct: 61 GATSYTHSLGLLELRQEICRHYLNYYGVKIVPDQVIVSSGTSPLMLLLFSTLLDQGDELI 120 Query: 121 LPSPYWVTYPEQIRFFGGVPVEVPLKKEKGFQLSLEDVKEKVTERTKAIVINSPNNPTGA 180 L P + YP ++F GG PV + + GFQ ++ VK +TE+T+ ++INSP+NP G+ Sbjct: 121 LTDPGYACYPGFVKFSGGAPVLLKTAAKDGFQPKVDQVKALMTEKTRGLLINSPSNPAGS 180 Query: 181 VYEEEELKKIAEFCVERGIFIISDECYEYFVY-GDAKFVSPASFSDEVKNITFTVNAFSK 239 V EE++ +A+ + IISDE Y Y G+ + + E F + FSK Sbjct: 181 VLSGEEMQALAQLPIP----IISDEIYHGLTYHGEERCIL------EFTENAFVLGGFSK 230 Query: 240 SYSMTGWRIGYVACPEEYAKVIASLNSQSVSNVTTFAQYGALEALKNPKSKDFVNEMRNA 299 +Y+MTGWR+G++ P + + +L+ + F Q G + AL+ + D V+ MR+ Sbjct: 231 AYAMTGWRLGFLISPLSCIRTLQTLHQNFLICANHFVQRGGIAALQ--QCDDEVDAMRSV 288 Query: 300 FERRRDTAVEELSKIPGMDVVKPEGAFYIFPDFSAYAEKLGGDVKLSEFLLEKAKVAVVP 359 +++RR V L ++ +P+GAFY+ D G +L+ +LEK VAV P Sbjct: 289 YDKRRIALVAGLRELGFGVHFEPQGAFYVLADARHID---GNSQRLALDILEKTGVAVTP 345 Query: 360 GSAF--GAPGFLRLSYALSEERLVEGIRRI 387 G F GA GFLR SY + ++R+ Sbjct: 346 GVDFGQGAEGFLRFSYTRPLTEITVALQRL 375 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: 362 Number of extensions: 19 Number of successful extensions: 5 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: 384 Length adjustment: 30 Effective length of query: 364 Effective length of database: 354 Effective search space: 128856 Effective search space used: 128856 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