Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate 3608039 Dshi_1446 aminotransferase class-III (RefSeq)
Query= SwissProt::Q8ZPV2 (408 letters) >FitnessBrowser__Dino:3608039 Length = 444 Score = 192 bits (489), Expect = 1e-53 Identities = 139/409 (33%), Positives = 202/409 (49%), Gaps = 49/409 (11%) Query: 26 VRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANR--FWHIGNGYTNEPA 83 V G G + D GK Y+D +GG AV+ LGH HPA+R AL+ Q ++ F H G +T+EPA Sbjct: 17 VAGAGCYIIDADGKRYLDGSGGAAVSCLGHDHPAVRAALHAQIDKIAFAHTGF-FTSEPA 75 Query: 84 LRLAKKLIDAT--FAERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAFHGR 141 L LI A E+V+ + G+E+ EAALKLAR++ + + ++A + ++HG Sbjct: 76 EVLCDALIAAAPKGIEKVYLLSGGSESVEAALKLARQFFLETGEPRRHRVIARRQSYHGN 135 Query: 142 TLFTVSAGGQPTYSQDFAPLPPDI---------RHAAYNDLNSA-------------SAL 179 TL ++AGG + +APL + RH A + ++A L Sbjct: 136 TLGALAAGGNAWRREKYAPLLVETYHIDPCYAYRHQAVGESDAAYGRRAADALRTEIERL 195 Query: 180 IDDNTCAVIVEPVQGE-GGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAY 238 + A I EPV G G +P + + +RE+CD + LLI DEV G+GRTG L+A Sbjct: 196 GPETVMAFIAEPVVGATAGAVPPAPGYFERIREICDEYGVLLILDEVMCGMGRTGTLFAC 255 Query: 239 MHYGVTPDILTTAKALGGGF-PIGAMLTTQDYASVMTPGT----HGTTYGGNPLATAVAG 293 G++PDI+T AK LG G+ PIGAML + + G+ HG TY G+PLA A AG Sbjct: 256 EQDGISPDIVTIAKGLGAGYAPIGAMLASGRIYDAIAQGSGSFQHGHTYHGHPLAAAAAG 315 Query: 294 KVLDIINTPEMQNGVRQRHDAFIERLNTLNVRFGMFSEIRGLGLLLGCVL--------QT 345 V++ + P VR + RL + +IRG GL G L Sbjct: 316 AVVETLRAPGTMAQVRAKGATLQSRLEAALGQHSHVGDIRGRGLFRGIELVEDRDTKRPL 375 Query: 346 EFAGKAKLIAQEAAKAGVMVLIAG--------GDVVRFAPALNVSDEEI 386 + A K + AA A ++ G GD + AP + D++I Sbjct: 376 DPARKVSARIKAAAMARGLICYPGSGTIDGKHGDHILLAPPFIIEDKQI 424 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: 484 Number of extensions: 18 Number of successful extensions: 4 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: 444 Length adjustment: 32 Effective length of query: 376 Effective length of database: 412 Effective search space: 154912 Effective search space used: 154912 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