Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate CCNA_00620 CCNA_00620 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase
Query= SwissProt::Q8ZPV2 (408 letters) >FitnessBrowser__Caulo:CCNA_00620 Length = 392 Score = 338 bits (868), Expect = 1e-97 Identities = 189/388 (48%), Positives = 235/388 (60%), Gaps = 9/388 (2%) Query: 14 MVPVYVPAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWH 73 ++ Y A VRGEG L+DQ G++Y+D A G+AVN LGH P L +AL QA+ WH Sbjct: 4 LMNTYARANIDIVRGEGCWLYDQDGRDYLDLAAGVAVNTLGHGDPRLVQALKTQADILWH 63 Query: 74 IGNGYTNEPALRLAKKLIDATFAERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVA 133 N Y LA KL DATFA+RVFF NSGAEA EAA+K AR++ + + ++ Sbjct: 64 ASNLYRLPAQEALATKLTDATFADRVFFANSGAEAVEAAIKTARRWQGAKGRPERYRVLT 123 Query: 134 FKNAFHGRTLFTVSAGGQPTYSQDFAPLPPDIRHAAYNDLNSASALIDDNTCAVIVEPVQ 193 F NAFHGRTL T+SA Q + F PL +ND+ A+ I T A++VEP+Q Sbjct: 124 FGNAFHGRTLATISATDQMKVREGFTPLYDAFDTTPFNDIEGAARAITPQTAAILVEPIQ 183 Query: 194 GEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPDILTTAKA 253 GEGG+ PAT FL GLR LCD+H LLI DEVQTG+GRTG L+A+ YGV PDI+ AK Sbjct: 184 GEGGLTPATPGFLAGLRALCDQHDLLLILDEVQTGIGRTGHLFAHELYGVRPDIIAVAKG 243 Query: 254 LGGGFPIGAMLTTQDYASVMTPGTHGTTYGGNPLATAVAGKVLDIINTPEMQNGVRQRH- 312 LGGGFPIGA L T+D AS MTPG+HG+TYGGNPLA AVA VLD + P VR+R Sbjct: 244 LGGGFPIGACLATEDAASGMTPGSHGSTYGGNPLACAVASAVLDAVLAPGFLETVRERAA 303 Query: 313 --DAFIERLNTLNVRFGMFSEIRGLGLLLGCVLQTEFAGKAKLIAQEAAKAGVMVLIAGG 370 DA +ERL L +F +G GL+ G + A+ + GVM + AG Sbjct: 304 LVDALLERL--LRRHSDLFVRAQGHGLMRG----LQVRASARDVVAHLRDFGVMTVAAGA 357 Query: 371 DVVRFAPALNVSDEEIATGLDRFALACE 398 DVVR P L +S+ EIA R A E Sbjct: 358 DVVRLLPPLTISELEIAEAEARLLRAAE 385 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: 455 Number of extensions: 16 Number of successful extensions: 2 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: 392 Length adjustment: 31 Effective length of query: 377 Effective length of database: 361 Effective search space: 136097 Effective search space used: 136097 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