Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate Echvi_2919 Echvi_2919 Ornithine/acetylornithine aminotransferase
Query= SwissProt::Q8ZPV2 (408 letters) >FitnessBrowser__Cola:Echvi_2919 Length = 393 Score = 218 bits (555), Expect = 2e-61 Identities = 129/369 (34%), Positives = 203/369 (55%), Gaps = 23/369 (6%) Query: 27 RGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWH--IGNGYTNEPAL 84 + EG ++ +G++YID GI V+ +GH HP + +A+ +Q +++ H + Y P Sbjct: 25 KAEGIYMYGPKGEKYIDLISGIGVSNVGHRHPKVLKAIQDQLDKYMHLMVYGEYVQSPQT 84 Query: 85 RLAKKLIDAT--FAERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAFHGRT 142 +LAK L D + V+ NSG+EA E ALKLA++Y R I++ NA+HG + Sbjct: 85 QLAKALTDTLPKKLDNVYLVNSGSEAVEGALKLAKRYTGRRE------ILSCVNAYHGSS 138 Query: 143 LFTVSAGGQPTYSQDFAPLPPDIRHAAYNDLNSASALIDDNTCAVIVEPVQGEGGVIPAT 202 +S GG + + + PL P IRH +N+ + + ++ T A++VE VQGE G+ T Sbjct: 139 HGALSVGGNEIFKRAYRPLLPGIRHLDFNEPDQLDQITEE-TAAIMVETVQGEAGIRVGT 197 Query: 203 KAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPDILTTAKALGGGFPIGA 262 K + + LR CD LLI DE+Q G GRTG+ +A+ HY + PDI+ AK +GGG PIGA Sbjct: 198 KEYFKALRHRCDETGTLLILDEIQAGFGRTGKFWAFQHYDIVPDIVVCAKGMGGGMPIGA 257 Query: 263 MLTTQDYASVMTPGT---HGTTYGGNPLATAVAGKVLDIINTPEMQNGVRQRHDAFIERL 319 + Q SV H TT+GG+P++ A A +DI+ ++ V ++ + F + L Sbjct: 258 FIAPQSIMSVFKNNPLLGHITTFGGHPVSCAAALATIDILRDEKLIQHVERKANLFKKHL 317 Query: 320 NTLNVRFGMFSEIRGLGLLLGCVLQTEFAGKAKLIAQEAAKAGVMV--LIAGGDVVRFAP 377 N ++ EIR GL++ ++ E K I A + G++ + D +R AP Sbjct: 318 NHPKIQ-----EIRNKGLMM--AVKFEAFEVLKPIIDRAIELGIITDWFLFCEDSMRIAP 370 Query: 378 ALNVSDEEI 386 L ++DEEI Sbjct: 371 PLTITDEEI 379 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: 402 Number of extensions: 22 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: 393 Length adjustment: 31 Effective length of query: 377 Effective length of database: 362 Effective search space: 136474 Effective search space used: 136474 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 Aug 03 2021. The underlying query database was built on Aug 03 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