Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate WP_013834987.1 THICY_RS02200 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::Q8ZPV2 (408 letters) >NCBI__GCF_000214825.1:WP_013834987.1 Length = 427 Score = 123 bits (308), Expect = 1e-32 Identities = 93/285 (32%), Positives = 131/285 (45%), Gaps = 23/285 (8%) Query: 29 EGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIGNGYTNEPALR-LA 87 +G+ L D+ K+YID+ G LGHAHP + A+ QA G E + L Sbjct: 40 KGAYLTDEDNKQYIDYVGSWGPAILGHAHPDVIAAVQRQAEFGLTFGAPTVMETTMADLV 99 Query: 88 KKLIDATFAERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAFHGRT--LFT 145 +L+ + E V +SG EA A++LAR Y G K IV F+ +HG + L Sbjct: 100 CELVPSI--EMVRMVSSGTEATMTAIRLARGYT----GRDK--IVKFEGCYHGHSDSLLV 151 Query: 146 VSAGGQPTYSQDFAPLPPD--------IRHAAYNDLNSASALIDDNTCAVIVEPVQGEGG 197 + G T +P PD + H +++ + I D +IVEPV G Sbjct: 152 KAGSGALTLGVPSSPGVPDSLANHTITLTHNDADEVRKVFSEIGDQVACIIVEPVAGNMN 211 Query: 198 VIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPDILTTAKALGGG 257 I FL+ LRE+CD H ++LIFDEV G R G A YGV D+ T K +GGG Sbjct: 212 CILPEPGFLETLREVCDEHGSVLIFDEVMCGF-RVGLQGAQGRYGVQADLTTYGKVIGGG 270 Query: 258 FPIGAM---LTTQDYASVMTPGTHGTTYGGNPLATAVAGKVLDII 299 P+GA + + + P T GNP+A A L ++ Sbjct: 271 MPVGAFGGKKAIMSHIAPLGPVYQAGTLSGNPIAMAAGLTTLHML 315 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: 451 Number of extensions: 22 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 408 Length of database: 427 Length adjustment: 32 Effective length of query: 376 Effective length of database: 395 Effective search space: 148520 Effective search space used: 148520 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 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