Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate CCNA_01648 CCNA_01648 adenosylmethionine-8-amino-7-oxononanoate
Query= SwissProt::Q8ZPV2 (408 letters) >FitnessBrowser__Caulo:CCNA_01648 Length = 420 Score = 155 bits (393), Expect = 2e-42 Identities = 131/394 (33%), Positives = 188/394 (47%), Gaps = 39/394 (9%) Query: 20 PAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIG-NGY 78 P P + RG +RL + G+E +D G+ HP + AL +Q H+ G Sbjct: 27 PLPVVATRG--ARLILEDGRELVDGLASWWTACHGYNHPHIAGALRKQIETMPHVMFGGL 84 Query: 79 TNEPALRLAKKLIDATFAE--RVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKN 136 +EPA RLAK+L + VFF SG+ A E A+K+A +Y +R ++ +AF+ Sbjct: 85 AHEPAYRLAKRLARLLPGDLDHVFFAESGSVAVEIAMKMALQYQINRGVGGRTRFLAFRG 144 Query: 137 AFHGRTLFTVS------------AGGQPTYSQDFAPLPPDIRHAAYNDLNSASALIDDNT 184 +HG TL T++ AG P +Q A LP D A+ L++ A Sbjct: 145 GYHGDTLATMTVCDPEEGMHSLFAGVMP--AQVIADLPRD--PASEAALDALLAARGHEI 200 Query: 185 CAVIVEP-VQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGV 243 A++VEP +QG GG++P L+ LR L D+H LLIFDE+ TG GRTG L+A GV Sbjct: 201 AAMLVEPLIQGAGGMLPHPPEVLRTLRRLADKHGVLLIFDEIFTGFGRTGSLFAMQAAGV 260 Query: 244 TPDILTTAKAL-GGGFPIGAMLT---------TQDYASVMTPGTHGTTYGGNPLATAVAG 293 PDI+T +KAL GG P+ A + + D A+ + HG TY NPLA A A Sbjct: 261 EPDIVTLSKALTGGTLPLSAAVARRHVFEAFWSDDPAAAL---MHGPTYMANPLACAAAN 317 Query: 294 KVLDIINTPEMQNGVRQRHDAFIERLNTLNVRFGMFSEIRGLGLLLGCVLQTEFAGKAKL 353 LD+ V + A E L G+ ++R LG + V++ E Sbjct: 318 ASLDLFEDGAWARDVARVSAALAEGLEPCRAGEGVV-DVRTLGAI--GVVEFEAPVPVSD 374 Query: 354 IAQEAAKAGVMVLIAGGDVVRFAPALNVSDEEIA 387 + A GV + G VV PA DE+++ Sbjct: 375 LCARFAALGVWIR-PMGKVVYLTPAFTTPDEDLS 407 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: 423 Number of extensions: 28 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: 420 Length adjustment: 31 Effective length of query: 377 Effective length of database: 389 Effective search space: 146653 Effective search space used: 146653 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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