Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate Ac3H11_3991 Glutamate-1-semialdehyde aminotransferase (EC 5.4.3.8)
Query= BRENDA::O30508 (406 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3991 Length = 434 Score = 106 bits (264), Expect = 2e-27 Identities = 87/301 (28%), Positives = 140/301 (46%), Gaps = 22/301 (7%) Query: 30 RGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHVSNVFTNEPALRL 89 R +G+ WD + + ID+ G LGH HPA+++A+ Q+ + S E + L Sbjct: 42 RAQGAYFWDANDQRFIDYIGSWGPMILGHGHPAVLEAV--QSAALEGFSFGAPTEREVEL 99 Query: 90 ARKLVDATFA-ERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNSFHGRTLFT 148 A +++ + E + L +SG EA +A +LAR G K+ H +L Sbjct: 100 AEEILGLVPSMEMIRLVSSGTEAGMSAIRLAR----GATGRSKFIKFEGCYHGHADSLLV 155 Query: 149 VNVGGQPKYSDGF--GPKFEGITH---VPYNDLEALKAAIS---DKTCAVVLEPIQGEGG 200 G + + G E + H + YN++ L+ A + + V++EPI G Sbjct: 156 KAGSGLATFGNATSAGVPPEVVQHTIVLEYNNVAQLEEAFALHGKELACVMIEPIAGNMN 215 Query: 201 VLPAQQAYLEGARKLCDEHNALLVFDEVQSG----MGRVGELFAYMHYGVVPDILSSAKS 256 ++ A +++ R+LC EH ALLV DEV +G +G ++A G PD+ K Sbjct: 216 LVRASVPFMKRCRELCTEHGALLVLDEVMTGFRVALGSAQSVYAKSIPGFKPDLTVLGKV 275 Query: 257 LGGGFPIGAMLTTGEIAKHLSV--GTH-GTTYGGNPLASAVAEAALDVINTPEVLDGVKA 313 +GGG P+ A I +HL+ G + T GNP+A+A A L I P D + A Sbjct: 276 IGGGMPLAAFGGPRAIMEHLAPLGGVYQAGTLSGNPVATACGLATLREIKKPGFFDALSA 335 Query: 314 K 314 + Sbjct: 336 R 336 Lambda K H 0.318 0.135 0.394 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: 436 Number of extensions: 19 Number of successful extensions: 5 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: 406 Length of database: 434 Length adjustment: 32 Effective length of query: 374 Effective length of database: 402 Effective search space: 150348 Effective search space used: 150348 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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