Align Succinylornithine transaminase; SOAT; EC 2.6.1.81; Succinylornithine aminotransferase (uncharacterized)
to candidate WP_012505186.1 PAES_RS02955 aspartate aminotransferase family protein
Query= curated2:Q3Z295 (406 letters) >NCBI__GCF_000020625.1:WP_012505186.1 Length = 397 Score = 274 bits (701), Expect = 3e-78 Identities = 146/391 (37%), Positives = 214/391 (54%), Gaps = 4/391 (1%) Query: 1 MSQPITRENFDEWMIPVYAPAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPEL 60 M+ + +E E YA P G+G L+D+ Y+D GI VNALG+ L Sbjct: 1 MTSILNKETEHELFFHNYARLPLAITHGKGVYLFDENSNRYLDMISGIGVNALGYGDERL 60 Query: 61 REALNEQASKFWHTGNGYTNEPVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFA 120 EA+++QA K H N + EP +LA KL+D + +VFF NSG EA EAA+KL+RK+A Sbjct: 61 IEAIHDQAKKIIHASNLFMLEPQFKLASKLLDISGLSKVFFANSGTEAIEAAMKLSRKWA 120 Query: 121 HDRYGSHKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPDIRHAAYNDINSASALI 180 + K I++ N FHGRT +S +P Y + F PL P A+NDI I Sbjct: 121 SLSGSTGKKEILSLSNCFHGRTYGAMSLTAKPKYLEGFDPLLPGTGSIAFNDIEDLKRKI 180 Query: 181 DDATCAVIVEPIQGEGGVVPASNAFLQGLRELCDRHNALLIFDEVQTGVGRTGELYAYMH 240 T AV +E +QGEGG+ S F++ L++L + HN L++ DE+Q G GRTG+ ++YMH Sbjct: 181 TSNTAAVFIEFVQGEGGIHQISREFVEELKKLRETHNFLIVADEIQAGCGRTGKFFSYMH 240 Query: 241 YGVTPDLLTTAKALGGGFPVGALLTTEECASVMTVGTHGTTYGGNPLASAVAGKVLELIN 300 + + PDL+ AK LGGG P+GA++ + + V G HGTT+GGNP+A A ++E + Sbjct: 241 FDIDPDLVCVAKPLGGGLPLGAVIGSRKVQDVFAAGNHGTTFGGNPVACAAGHALIETLY 300 Query: 301 TPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAK 360 + +++ W L + + E+R GL+IG +N D A QE+ K Sbjct: 301 SKKIMEHALATGSWIKAALTKLAETHTQIQEIRQYGLMIGITVNRD----AAYYVQESLK 356 Query: 361 AGVMVLIAGGNVVRFAPALNVSEEEVTTGLD 391 V+V NV+R P L ++ EE +D Sbjct: 357 RRVLVNATSQNVIRLLPPLTITVEEAQQCID 387 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: 399 Number of extensions: 23 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: 397 Length adjustment: 31 Effective length of query: 375 Effective length of database: 366 Effective search space: 137250 Effective search space used: 137250 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