Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate WP_092053439.1 BQ4888_RS01605 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= SwissProt::Q8ZPV2 (408 letters) >NCBI__GCF_900111775.1:WP_092053439.1 Length = 449 Score = 170 bits (430), Expect = 9e-47 Identities = 141/420 (33%), Positives = 197/420 (46%), Gaps = 60/420 (14%) Query: 22 PFIPV-RGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRF-WHIGNGYT 79 P IP+ RG+G+ L+D GK YID VN GH HP L AL++QA + HI G+T Sbjct: 28 PPIPIARGDGAYLYDFDGKGYIDGVSSWWVNLFGHNHPRLNRALSKQAGKVAHHIFAGFT 87 Query: 80 NEPALRLAKKLIDAT--FAERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNA 137 +EPA LA +L + E+VFF ++G+ A EAALK++ +Y K+ V+ A Sbjct: 88 HEPAATLAARLCELAPPGLEKVFFTDNGSAAVEAALKMSFQYWRQTGQGEKTRFVSITEA 147 Query: 138 FHGRTLFTVSAGGQPTYSQDFAPL--------PPDIRHAAYN------------DLNSAS 177 +HG TL +S GG Y + PL PD Y + Sbjct: 148 YHGETLGALSVGGCGLYKDIYQPLLLDGFQVQGPDCFRCPYGCERESCNAECFAAMEEVV 207 Query: 178 ALIDDNTCAVIVEP-VQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELY 236 A AVI+EP +Q G+ +L+ LRELCDR + I DE+ G GRTG L+ Sbjct: 208 AEHHRQIAAVIIEPLIQCAAGMRIYPPIYLKKLRELCDRWRIHYIADEIAVGFGRTGRLF 267 Query: 237 AYMHYGVTPDILTTAKALGGGF-PIGAMLTTQ--------DYASVMTPGTHGTTYGGNPL 287 A H GV+PD+L +K + GG+ P+ +LT Q DYA+ + H +Y GNPL Sbjct: 268 ANEHAGVSPDLLCLSKGITGGYMPLSVVLTRQEMYDAFYDDYAT-LKAFLHSHSYSGNPL 326 Query: 288 ATAVAGKVLDIIN--------TPEMQNGVRQRHDAFIERLNTLNVRFGMFSEIRGLGLLL 339 A A+A +VL+I P+M Q+H R L E R LGL+ Sbjct: 327 ACALACEVLNIFTEEKILEKMVPKMAILASQKH-----RFEAL----PQVGEFRQLGLVG 377 Query: 340 GCVLQTEFAGKAKLIAQEAAKAGV--------MVLIAGGDVVRFAPALNVSDEEIATGLD 391 L + GK QE V +L G+VV F P L + +++ +D Sbjct: 378 AIELVRDKVGKTPYPWQERRGYAVYRKALEKGALLRPLGNVVYFMPPLTIEKADLSRLVD 437 Lambda K H 0.320 0.137 0.413 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: 456 Number of extensions: 24 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: 408 Length of database: 449 Length adjustment: 32 Effective length of query: 376 Effective length of database: 417 Effective search space: 156792 Effective search space used: 156792 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: 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