Align Succinylornithine transaminase; SOAT; EC 2.6.1.81; Succinylornithine aminotransferase (uncharacterized)
to candidate WP_041466176.1 CPAR_RS07660 aspartate aminotransferase family protein
Query= curated2:Q3Z295 (406 letters) >NCBI__GCF_000020505.1:WP_041466176.1 Length = 402 Score = 270 bits (689), Expect = 7e-77 Identities = 144/378 (38%), Positives = 209/378 (55%), Gaps = 4/378 (1%) Query: 18 YAPAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNG 77 YA P +GS L+ G Y+D GI VNA+G+ L A+ EQA+K+ H N Sbjct: 19 YARLPLDIAYAKGSFLYTSGGDRYLDMIAGIGVNAIGYGDQRLEHAITEQAAKYIHVSNL 78 Query: 78 YTNEPVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNA 137 + +P LA L++ + +VFFCNSG EA EAA+KLAR+FA + K+ +++ N Sbjct: 79 FMQKPQFDLAATLLEISGMSKVFFCNSGTEAIEAAIKLARRFAARNGDTSKTQVLSLTNC 138 Query: 138 FHGRTLFTVSAGGQPAYSQDFAPLPPDIRHAAYNDINSASALIDDATCAVIVEPIQGEGG 197 FHGRT +S +P Y F PL P+ +N+I + T AV VE +QGEGG Sbjct: 139 FHGRTYGALSLTAKPKYVGGFEPLVPETGMIDFNNIEDLERKVSSRTAAVFVEFVQGEGG 198 Query: 198 VVPASNAFLQGLRELCDRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLTTAKALGGG 257 + S AF+ L+EL H+ L++ DE+Q G GRTG ++YM + + PDL+ AK LGGG Sbjct: 199 IHKVSEAFIARLKELAAEHDFLIVADEIQAGCGRTGSFFSYMPFDIQPDLVCVAKPLGGG 258 Query: 258 FPVGALLTTEECASVMTVGTHGTTYGGNPLASAVAGKVLELINTPEMLNGVKQRHDWFVE 317 P+GA++ TE+ A V T G+HGTT+GGNP+A A ++E I +++ + Sbjct: 259 LPLGAIIGTEKVAEVFTPGSHGTTFGGNPVACAAGLAMIEAIKADKLMENAIETGAMMRA 318 Query: 318 RLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVMVLIAGGNVVRFAP 377 + ++ E+R GL+IG +N +AK EA K V+V NV+R P Sbjct: 319 AFEKMAEKHAQILEIRQYGLMIGITVNR----EAKYYVDEALKRNVLVNATSQNVIRLLP 374 Query: 378 ALNVSEEEVTTGLDRFAA 395 L++S+EE LD A Sbjct: 375 PLSISKEEAQLCLDTLDA 392 Lambda K H 0.319 0.136 0.408 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: 401 Number of extensions: 20 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: 406 Length of database: 402 Length adjustment: 31 Effective length of query: 375 Effective length of database: 371 Effective search space: 139125 Effective search space used: 139125 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 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