Align Acetylornithine aminotransferase; Short=ACOAT; EC 2.6.1.11 (characterized, see rationale)
to candidate WP_005457886.1 SACCYDRAFT_RS16640 acetylornithine transaminase
Query= uniprot:A0A806JQF3 (400 letters) >NCBI__GCF_000244975.1:WP_005457886.1 Length = 395 Score = 467 bits (1202), Expect = e-136 Identities = 234/383 (61%), Positives = 283/383 (73%), Gaps = 1/383 (0%) Query: 14 RWQAVMMNNYGTPPIALASGDGAVVTDVDGRTYIDLLGGIAVNVLGHRHPAVIEAVTRQM 73 RW++VMMNNYGTP + L G+GAVV D DGR Y+D + GIAVN LGH HPAV+ AVTRQ+ Sbjct: 9 RWRSVMMNNYGTPAVNLVRGEGAVVWDADGRRYLDFVTGIAVNALGHAHPAVVSAVTRQI 68 Query: 74 STLGHTSNLYATEPGIALAEELVALLGADQRTRVFFCNSGAEANEAAFKLSRLTGRTKLV 133 +T+GHTSNLY EP + LAE L+ L GA +V FCNSGAEA EAAFKL+R TGR+ +V Sbjct: 69 ATIGHTSNLYLNEPALTLAERLLELSGAGDG-KVLFCNSGAEAVEAAFKLARRTGRSTVV 127 Query: 134 AAHDAFHGRTMGSLALTGQPAKQTPFAPLPGDVTHVGYGDVDALAAAVDDHTAAVFLEPI 193 A FHGRTMG+LALTGQPAK+ PF PL V HV +GDV AL A+D TAA +EP+ Sbjct: 128 ATEGGFHGRTMGALALTGQPAKRAPFEPLVPGVRHVPFGDVPALERAIDSDTAAFVVEPV 187 Query: 194 MGESGVVVPPAGYLAAARDITARRGALLVLDEVQTGMGRTGAFFAHQHDGITPDVVTLAK 253 GE+GVVVP YL AAR+IT R G LLV+DEVQTG+GR G++FA+Q GI PDVVTLAK Sbjct: 188 QGENGVVVPGDDYLRAAREITRRHGVLLVVDEVQTGVGRLGSWFAYQQTGIQPDVVTLAK 247 Query: 254 GLGGGLPIGACLAVGPAAELLTPGLHGSTFGGNPVCAAAALAVLRVLASDGLVRRAEVLG 313 GLGGGLP+GACLA G AA L PG HG+TFGGNPVC AA LAVL +A++GL+ LG Sbjct: 248 GLGGGLPLGACLAFGEAATLFEPGQHGTTFGGNPVCCAAGLAVLDTIAANGLLEHTAALG 307 Query: 314 KSLRHGIEALGHPLIDHVRGRGLLLGIALTAPHAKDAEATARDAGYLVNAAAPDVIRLAP 373 K + G+E L HPL+ VRG GLLLG+ L + + A A+ AG+LVN PDV+RLAP Sbjct: 308 KEISAGLERLDHPLVRTVRGAGLLLGVVLNSAVSAGVAAAAQRAGFLVNPVQPDVVRLAP 367 Query: 374 PLIIAEAQLDGFVAALPAILDRA 396 PL++++ Q D +AALPA D A Sbjct: 368 PLVVSQEQADALLAALPAAFDAA 390 Lambda K H 0.320 0.136 0.399 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: 511 Number of extensions: 16 Number of successful extensions: 2 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: 400 Length of database: 395 Length adjustment: 31 Effective length of query: 369 Effective length of database: 364 Effective search space: 134316 Effective search space used: 134316 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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