Align Succinylornithine transaminase; SOAT; EC 2.6.1.81; Succinylornithine aminotransferase (uncharacterized)
to candidate WP_080517386.1 RSPH17029_RS20165 aspartate aminotransferase family protein
Query= curated2:Q3Z295 (406 letters) >NCBI__GCF_000015985.1:WP_080517386.1 Length = 461 Score = 161 bits (407), Expect = 4e-44 Identities = 125/419 (29%), Positives = 204/419 (48%), Gaps = 43/419 (10%) Query: 22 PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASK--FWHTGNGYT 79 P I RG+G ++D +G+EYI+ G+ A+G + P L EA Q ++ ++HT G Sbjct: 32 PLIITRGQGVHVYDSEGREYIEGLAGLWSVAVGFSEPRLAEAAARQMAELPYYHTFAGKA 91 Query: 80 NEPVLRLAKKLIDAT--FADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNA 137 +EP +RLA+KL++ T RVFF NSG+EAN+ +KL + K ++ Sbjct: 92 HEPQIRLAEKLVEMTPVALTRVFFTNSGSEANDTVVKLVWFMNNALGRPQKKKFLSRIKG 151 Query: 138 FHGRTLFTVSAGGQPAYSQDF-APLPPDI-----RHAAY-----NDINSASALIDDA--- 183 +HG T+ + S G P + F P P + H + ++ + + L+ +A Sbjct: 152 YHGITIASGSLTGLPVNHKGFDLPAIPVVHLGCPHHWRFGAEGESEADFCARLLREAEET 211 Query: 184 --------TCAVIVEPIQGEGGVVPASNAFLQGLRELCDRHNALLIFDEVQTGVGRTGEL 235 A I EP+ G GGV+ + + G+ LC +++ LL+ DEV G GRTG Sbjct: 212 ILAEGPETVAAFIGEPVMGAGGVIVPPDGYWSGIEALCRKYDILLVSDEVINGFGRTGAR 271 Query: 236 YAYMHYGVTPDLLTTAKALGGGF-PVGALLTTEECASVM-----TVGT--HGTTYGGNPL 287 + +G TPD+L T+K L + P+ A+L T++ ++ TVGT HG T G+P+ Sbjct: 272 WGCEKFGFTPDILVTSKQLTSSYMPLAAVLMTDKVYQIIADHTETVGTLGHGFTGSGHPV 331 Query: 288 ASAVAGKVLELINTPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADY 347 A+AV + L +I +++ + F + L L EVRG GL+ + AD Sbjct: 332 ATAVGLENLTVIEERDLMGNAARLERPFQDGLRAFRDN-PLVGEVRGTGLIAAIEMVADR 390 Query: 348 AGQA--KQISQEAAKAGVMVLIAG------GNVVRFAPALNVSEEEVTTGLDRFAAACE 398 A + + + + A+A G G+ + P L V+E +V L+R A + Sbjct: 391 ATKRSFEPLGKVGARAAAFAAEEGLLCRALGDTLALCPPLIVTEADVGGILERMGRALD 449 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: 484 Number of extensions: 29 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 406 Length of database: 461 Length adjustment: 32 Effective length of query: 374 Effective length of database: 429 Effective search space: 160446 Effective search space used: 160446 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 16 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