Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate WP_024850313.1 N745_RS0101155 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= SwissProt::Q8ZPV2 (408 letters) >NCBI__GCF_000526715.1:WP_024850313.1 Length = 442 Score = 157 bits (397), Expect = 6e-43 Identities = 124/389 (31%), Positives = 201/389 (51%), Gaps = 35/389 (8%) Query: 29 EGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIG-NGYTNEPALRLA 87 +GS + G E +D G+ HP +++A++EQ + HI G T+EPA+ L+ Sbjct: 43 QGSVITLADGTELVDGMSSWWAALHGYNHPKIQQAMHEQIDIMPHIMFGGLTHEPAIELS 102 Query: 88 KKLIDAT--FAERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAFHGRTLFT 145 K+L+ T ++VF +SG+ A E A+K+A +Y + +K+ ++ +N +HG T T Sbjct: 103 KRLVKLTPEGLDKVFLVDSGSVAMEVAIKMALQYWVSKDQPNKNRLLTVRNGYHGDTFAT 162 Query: 146 VSA-----GGQPTYSQD-----FAPLPP---DIRHAAYNDLNSASALIDD---NTCAVIV 189 ++ G +S+ FAP P DI + D+NS ++++ N AV + Sbjct: 163 MAVCDPVNGMHSLFSEILTQHYFAPEPEMGFDIE-SDNQDINSLKTMLEEHHNNIAAVTI 221 Query: 190 EP-VQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPDIL 248 EP VQG GG+ +L+ LR+LCD + LLI DE+ TG GRTG+L+A G+TPDI+ Sbjct: 222 EPIVQGAGGMRFYRPDYLKQLRQLCDEYGVLLIADEIATGFGRTGKLFACEWAGITPDIM 281 Query: 249 TTAKAL-GGGFPIGAMLTTQDYASV-------MTPG--THGTTYGGNPLATAVAGKVLDI 298 T K L GG + A L T D + + PG HG T+ GNPLA A A +D+ Sbjct: 282 TLGKTLTGGHISLAATLATTDVSDTISSNVGDLNPGLLMHGPTFMGNPLACAAAIANIDV 341 Query: 299 INTPEMQNGVRQRHDAFIERLNTLNVRFGMFSEIRGLGLLLGCVLQTEFAGKAKLIAQEA 358 + Q+ +++ + F E L L G+ ++ R LG + V++ E + + + Sbjct: 342 LMNSPWQDNIQRIEEHFTETLLPLKELEGV-ADARVLGAI--GVIELERSDLGPQVQAKG 398 Query: 359 AKAGVMVLIAGGDVVRFAPALNVSDEEIA 387 + G+ L G +V PA N+S ++ Sbjct: 399 IENGIW-LRPFGRLVYTMPAYNISQSNLS 426 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: 415 Number of extensions: 25 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: 442 Length adjustment: 32 Effective length of query: 376 Effective length of database: 410 Effective search space: 154160 Effective search space used: 154160 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