Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate 208056 DVU2559 adenosylmethionine--8-amino-7-oxononanoate aminotransferase
Query= SwissProt::Q8ZPV2 (408 letters) >MicrobesOnline__882:208056 Length = 542 Score = 172 bits (437), Expect = 2e-47 Identities = 137/416 (32%), Positives = 202/416 (48%), Gaps = 57/416 (13%) Query: 22 PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWH---IGNGY 78 P I +G+ L D G Y+D + N GH HP + EA+ Q +R H +G G Sbjct: 84 PCIIDAADGNHLIDTDGNRYLDGVSSLWTNVHGHRHPHIDEAIRRQLDRVAHSTLLGLGG 143 Query: 79 TNEPALRLAKKL--IDATFAERVFFCNSGAEANEAALKLARKYAHDRVGN--HKSGIVAF 134 T P++ LA +L I RVF+ +SG+ A EAALK+A +Y ++ ++AF Sbjct: 144 T--PSIELAARLTAIAPAGLTRVFYSDSGSTAVEAALKIAFQYHRQAPEGDARRTRVMAF 201 Query: 135 KNAFHGRTLFTVSAGGQPTYSQDFAPL---------------PPDIRH-----AAYNDLN 174 NA+HG T+ +VS GG + + PL P D+R A ++ Sbjct: 202 SNAYHGDTIGSVSLGGMSLFHGIYGPLLFDPVRAPAPHCYRCPADLRPETCGMACLGEVE 261 Query: 175 SASALIDDNTCAVIVEP-VQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTG 233 CAV+VEP VQG G++ + +L+GLR+LCDRH ++ DEV G G+TG Sbjct: 262 RLMRHHGHELCAVVVEPLVQGAAGMLVQPRGWLRGLRDLCDRHGVFMVADEVAVGFGKTG 321 Query: 234 ELYAYMHYGVTPDILTTAKALGGGF-PIGAMLTTQ--------DYASVMTPGTHGTTYGG 284 ++A GV PD+L AK + GG+ P+ A L T+ YA T HG TY G Sbjct: 322 TMFACEQEGVVPDMLCLAKGITGGYLPLAATLVTEHIHDGFLGGYADFRT-FFHGHTYTG 380 Query: 285 NPLATAVAGKVLDIINTPEMQNGVRQRHDAFIERLNTLNVRFG---MFSEIRGLGLLLGC 341 N LA A A LD+ +R R IERL TL +IR +G++ G Sbjct: 381 NALACAAALASLDVFEEERTLETLRPR----IERLATLLAPLNDLPHVGDIRRVGVMTGI 436 Query: 342 VL------QTEFAGKAKL---IAQEAAKAGVMVLIAGGDVVRFAPALNVSDEEIAT 388 L +T + + ++ + EA + GV+V GDV+ P L++++ E+ T Sbjct: 437 ELVADRETRTPYRPEERIGHRVTLEARRRGVIVRPL-GDVMVLMPPLSITETELET 491 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: 636 Number of extensions: 37 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: 542 Length adjustment: 33 Effective length of query: 375 Effective length of database: 509 Effective search space: 190875 Effective search space used: 190875 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