Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate WP_012504789.1 PAES_RS00970 glutamate-1-semialdehyde 2,1-aminomutase
Query= SwissProt::Q8ZPV2 (408 letters) >NCBI__GCF_000020625.1:WP_012504789.1 Length = 431 Score = 138 bits (348), Expect = 3e-37 Identities = 103/325 (31%), Positives = 147/325 (45%), Gaps = 30/325 (9%) Query: 22 PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIGNGYTN- 80 P +G+G+ + D G Y+D+ G LG HP + AL + IG + Sbjct: 36 PIYMAKGQGAYMTDVDGNTYLDYVGSWGPFILGSMHPRITAALEHTLTK---IGTSFGTP 92 Query: 81 -EPALRLAKKLIDATFA-ERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAF 138 E + +A+ L + E V NSG EA +A++LAR Y + I+ F+ + Sbjct: 93 IEMEIEIAELLCQIVPSIEMVRMVNSGTEATMSAVRLARGYTS------RDKIIKFEGCY 146 Query: 139 HGR-TLFTVSAG------GQPTYSQDFAPLPPDIRHAAYNDLNSASALIDDNT---CAVI 188 HG F + AG G P D +A YND+ S L+++N A+I Sbjct: 147 HGHGDSFLIKAGSGALTLGAPDSPGVTKGTANDTLNAKYNDIESVRLLVNENKGNIAAII 206 Query: 189 VEPVQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPDIL 248 +EPV G GVIPA FLQ LR+LC +LIFDEV G R A YGVTPD+ Sbjct: 207 IEPVAGNTGVIPAKPGFLQALRDLCTEEGIVLIFDEVMCGF-RVALGGAQERYGVTPDLT 265 Query: 249 TTAKALGGGFPIGAMLTTQDYASVMTP---GTHGTTYGGNPLATAVAGKVLDIINT---- 301 T K +GGG P+GA ++ + P T GNPLA + L I+ Sbjct: 266 TMGKIIGGGLPVGAFGGKREIMERIAPLGDVYQAGTLSGNPLALTAGLETLKILRDENPY 325 Query: 302 PEMQNGVRQRHDAFIERLNTLNVRF 326 PE++ + F +N L + + Sbjct: 326 PELERKAAFLEEGFRNNMNKLGLNY 350 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: 427 Number of extensions: 30 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: 431 Length adjustment: 32 Effective length of query: 376 Effective length of database: 399 Effective search space: 150024 Effective search space used: 150024 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