Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate GFF2981 HP15_2925 adenosylmethionine-8-amino-7-oxononanoate transaminase
Query= SwissProt::Q8ZPV2 (408 letters) >FitnessBrowser__Marino:GFF2981 Length = 450 Score = 156 bits (394), Expect = 1e-42 Identities = 126/410 (30%), Positives = 188/410 (45%), Gaps = 50/410 (12%) Query: 22 PFIPV-RGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWH-IGNGYT 79 P +P+ RGEG L D +G +ID VN GHA+P + A+ +Q H I G+T Sbjct: 29 PLVPIKRGEGVWLEDFEGNRFIDAVSSWWVNLFGHANPRINAAIQKQIGELEHVILAGFT 88 Query: 80 NEPALRLAKKLIDAT--FAERVFFCNSGAEANEAALKLARKY--AHDRVGNHKSGIVAFK 135 +EP + L+++LI+ T +VF+ ++G+ A EAALK++ Y HD+ G K V Sbjct: 89 HEPVVNLSERLIEVTPPGLNKVFYADNGSSAIEAALKMSFHYWKNHDKPG--KKNFVNLS 146 Query: 136 NAFHGRTLFTVSAGGQPTYSQDFAPLPPDIRHAAYND--------------------LNS 175 N++HG TL ++ G Y + PL ++ A D + Sbjct: 147 NSYHGETLGALALGDVSLYKDTYQPLLMEVLTAPSPDAFNKEPGETDEDYALRQFEAMEK 206 Query: 176 ASALIDDNTCAVIVEP-VQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGE 234 A + CAV+VEP +Q GG+ + LRE CDR+ LI DE+ G GRTG Sbjct: 207 LLAEKHEEICAVVVEPLIQCAGGMRMHHPIYHTKLREACDRYGVHLIADEIAVGFGRTGT 266 Query: 235 LYAYMHYGVTPDILTTAKALGGGF-PIGAMLTTQDYAS-------VMTPGTHGTTYGGNP 286 L+A G+TPD + +K L G+ P+ +LTT D + + H +Y GNP Sbjct: 267 LFACEQSGITPDFMCLSKGLTAGYLPLSVVLTTDDVYNAFYDDYETLKAFLHSHSYTGNP 326 Query: 287 LATAVAGKVLDIINTPEMQNGVRQRHDAFIERLNTLNVRFGMFSEIRGLGLLLGCVLQTE 346 + AVA LDI + R E + L +IR G+ L + + Sbjct: 327 IGCAVALATLDIFRDDNVIESNRALSTCMAESVAHL-ADHPNVGDIRQHGMTLAVEMVKD 385 Query: 347 FAGKAKLIAQEAAKAGVMV----------LIAGGDVVRFAPALNVSDEEI 386 A K QE + G+ V L G+VV F P +++E+I Sbjct: 386 KASKTPFPWQE--RRGIRVYQHALTRQALLRPLGNVVYFMPPYVITEEQI 433 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: 448 Number of extensions: 30 Number of successful extensions: 6 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: 450 Length adjustment: 32 Effective length of query: 376 Effective length of database: 418 Effective search space: 157168 Effective search space used: 157168 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 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