Align N-succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate WP_013009803.1 DACET_RS02325 glutamate-1-semialdehyde-2,1-aminomutase
Query= reanno::Btheta:353284 (373 letters) >NCBI__GCF_000025725.1:WP_013009803.1 Length = 422 Score = 132 bits (333), Expect = 1e-35 Identities = 96/304 (31%), Positives = 157/304 (51%), Gaps = 23/304 (7%) Query: 14 IVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATLGFYSNSVINKLQQ 73 + +G KV+DENG EY+D + GHA P ++ + + A LG S K + Sbjct: 32 VKSAKGSKVYDENGKEYIDYVCSWGPMITGHADPDIIKAVKD-AADLGT-SFGAPTKAEL 89 Query: 74 QVAERLGKISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFSKAFHGRT-SLAVE 132 +A+++ + + + L++SG EA +A++LA Y R K+I F +HG + SL V+ Sbjct: 90 DIAKKICSMVPSVEM-VRLVSSGTEALMSAIRLARAYTERDKIIKFEGCYHGHSDSLLVK 148 Query: 133 ATNNPTII-------APINNNGHVTYLPLNDIEAMKQELA--KGDVCAVIIEGIQGVGGI 183 A + P + H NDIE++K+ LA KG+V ++IE + G+ Sbjct: 149 AGSGALTFNQPSSPGVPADFTKHTLVAQYNDIESIKKLLAENKGEVACILIEPVAANMGV 208 Query: 184 KIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITVAKGIGNGF 243 +P F+++LR+VC + G +L+ DE+ +G+ R A +Y +I+PDI T+ K IG G Sbjct: 209 VLPAAGFLEDLRRVCDDEGVVLLFDEVITGF-RLAAGGAQEYFNIKPDITTMGKIIGGGL 267 Query: 244 PMAGV----LISPMFKP---VYGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKAVGD 296 P+ I M P VY Q G T GN LA +A L +++ + Q + +N + D Sbjct: 268 PVGAFGGKSEIMKMLSPDGAVY-QAG-TLSGNPLATAAGLTMLNKLSQPDFYKNLRQKAD 325 Query: 297 YLLE 300 L + Sbjct: 326 TLFD 329 Lambda K H 0.320 0.139 0.403 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: 335 Number of extensions: 17 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: 373 Length of database: 422 Length adjustment: 31 Effective length of query: 342 Effective length of database: 391 Effective search space: 133722 Effective search space used: 133722 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