Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate WP_012170173.1 AZC_RS08540 aspartate aminotransferase family protein
Query= SwissProt::Q8ZPV2 (408 letters) >NCBI__GCF_000010525.1:WP_012170173.1 Length = 472 Score = 130 bits (328), Expect = 6e-35 Identities = 113/429 (26%), Positives = 182/429 (42%), Gaps = 62/429 (14%) Query: 18 YVPAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIGNG 77 Y P I R EGS ++D + + ++D + G+ + L +A+ Q R + + Sbjct: 37 YTEFPKIFERCEGSFMYDDEDRPFLDLQMWYSAVNFGYGNQRLNDAMRRQLERLPQVASQ 96 Query: 78 YTNEPALRLAKKLIDATFAE-----RVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIV 132 Y + + LA ++ RV F GA+A E +LK+ R KS + Sbjct: 97 YLHREKIELAAEIAIGAQERFGRKGRVHFNVGGAQAIEDSLKIVRNAC-----GGKSLMF 151 Query: 133 AFKNAFHGRTLFTVSAGGQPTYSQ---------DFAPLPPDIR----------------- 166 AF+ +HGRTL + Y + F P R Sbjct: 152 AFEGGYHGRTLGASAITSSYRYRRRYGHFGERAQFVEFPYHFRGPRGMSKEEYGLHCVRK 211 Query: 167 -----HAAYNDLNSASALIDDNTCAVIVEPVQGEGGVIPATKAFLQGLRELCDRHQALLI 221 + YN + + A VEP+QG GG + F L+ + D+H LL+ Sbjct: 212 FERLFESEYNGVWDPK-VGQSEYAAFYVEPIQGTGGYVIPPANFFPELKRVLDKHGILLV 270 Query: 222 FDEVQTGVGRTGELYAYMHYGVTPDILTTAKALGGGF-PIGAMLTTQDYAS--VMTPGTH 278 DE+Q G RTG+L++ H+GV PD+L KAL G P+ + ++ + + G+ Sbjct: 271 VDEIQMGFFRTGKLWSIEHFGVQPDVLVFGKALTNGLNPLSGVWAREELINPQIFPAGST 330 Query: 279 GTTYGGNPLATAVAGKVLDIINTPEMQNGVRQRHDAFIERLNTLNVRFGMFSEIRGLGLL 338 +T+ NPL TAVA + + ++ + V ++ F+E + L + + ++ GLGL Sbjct: 331 HSTFNANPLGTAVALEAMRMMQEEDFGASVMEKGAHFLEGIKELKKKHAIVGDVDGLGLA 390 Query: 339 LG---CVLQTEFAGKAKLI---AQEAAKAGV--------MVLIAGG---DVVRFAPALNV 381 L C + KL+ A EA K + +VL GG +V+ APAL + Sbjct: 391 LRIEICEPHDSYTPSKKLVDLMADEAMKGDLVYGGERYGLVLDIGGYHKNVITLAPALTI 450 Query: 382 SDEEIATGL 390 S EI L Sbjct: 451 SHAEIDMAL 459 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: 507 Number of extensions: 34 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 408 Length of database: 472 Length adjustment: 32 Effective length of query: 376 Effective length of database: 440 Effective search space: 165440 Effective search space used: 165440 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