Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_090442076.1 BLS63_RS07545 diaminobutyrate--2-oxoglutarate transaminase
Query= curated2:Q8FTN2 (402 letters) >NCBI__GCF_900100495.1:WP_090442076.1 Length = 459 Score = 224 bits (572), Expect = 3e-63 Identities = 156/443 (35%), Positives = 223/443 (50%), Gaps = 59/443 (13%) Query: 8 EDTLTSWPQVLLNTYGTPPVELVTGKGSTVTDADGNVYIDLLAGIAVNALGHAHPAIIEA 67 E + S+P+ L P+ + +G VTD +GN Y+D LAG ALGH HP ++ + Sbjct: 27 ESNVRSYPRKL-------PLAIAKAEGVWVTDVEGNTYLDCLAGAGTLALGHNHPEVVAS 79 Query: 68 VTTQLSQLGHVSNLFATRPVVEVAAELVQRFALDDATIASQTQVFFCN-SGAEANEAAFK 126 + L+ + L T P+ + +E + + + FC SGA+A EAA K Sbjct: 80 LNDFLASGMPMHTLDLTTPLKDAFSETLLHLLPGNGR---DYCLQFCGPSGADAVEAALK 136 Query: 127 LAR-LTGRHRILAATNGFHGRTMGSLALTGQPDKRIPFAPLPSGVEFYPYGD-------- 177 LA+ +TGR IL+ + G+HG T G+LA+TG + L GV+F PY Sbjct: 137 LAKTVTGRSNILSFSGGYHGMTHGALAVTGNAAPKNAIHTLMPGVQFLPYPHEYRCPLGI 196 Query: 178 ---------LDYLTTL---VESDPTDTAAIILEPIQGETGVIPAPEGFLTGVRELCDKHG 225 + Y T VES + AA+ILE +QGE GV PAP G+L +RE+ KHG Sbjct: 197 GGEAGVQALMHYFTQFIEDVESGVSLPAAVILEAVQGEGGVNPAPSGWLRSIREVTRKHG 256 Query: 226 LLFIVDEVQTGIGRTGDFFAHQHEGVTPDVVTMAKGLGGGLPIGACLATGEAAKLFGPGK 285 +L I+DEVQ G RTG FA +H G+ PD++ M+K +GGGLP+ A L + PG Sbjct: 257 ILLILDEVQAGFARTGKMFAFEHAGIEPDIIVMSKAVGGGLPM-ALLGIKRQFDAWAPGA 315 Query: 286 HGTTFGGNPVSAAAARAVLSVIDEE-FCADVARKGELFAEQL----RGVAGVADVRGRGL 340 H TF GN ++ AA L V+ + A R+G +QL + + VRGRGL Sbjct: 316 HTGTFRGNQMAMAAGMTTLEVLQRQALTAQAERRGNWLKQQLTLLQQRYPALGQVRGRGL 375 Query: 341 MLGV---------------VLDQPVAKQAVTAGFKHGLILNAPA--DNIIRLTPPLVITD 383 MLG+ +D +A F HGL+L N++RL PPL+I + Sbjct: 376 MLGIEIVDERQRPDGLHSYPMDARLAAAIQQHCFSHGLLLERGGRNGNVVRLLPPLIIDE 435 Query: 384 DE----IRDAVRALAAVLAELNA 402 ++ I +AL A LA+L A Sbjct: 436 EQCALLIARFEQALIAALAQLRA 458 Lambda K H 0.319 0.137 0.398 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: 451 Number of extensions: 24 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: 402 Length of database: 459 Length adjustment: 32 Effective length of query: 370 Effective length of database: 427 Effective search space: 157990 Effective search space used: 157990 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