Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_012506718.1 PAES_RS10875 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_000020625.1:WP_012506718.1 Length = 428 Score = 134 bits (338), Expect = 4e-36 Identities = 99/309 (32%), Positives = 155/309 (50%), Gaps = 32/309 (10%) Query: 23 PAAFIPV-RGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHVS-NV 80 P PV R G + + GR+L+D G+ HP L A+T Q + HV Sbjct: 24 PLPVYPVARASGVTIELEDGRKLVDGMSSWWAAVHGYNHPVLNHAVTRQLDSMSHVMFGG 83 Query: 81 FTNEPALRLARKLVDATFA--ERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAAS 138 T+EPA++LA +L++ T ++VF ++SG+ + E A K+A +Y +K ++ Sbjct: 84 LTHEPAVKLAGQLIELTPEPLQKVFFSDSGSVSVEVAIKMALQYWQAAGLSRKRRLLTVR 143 Query: 139 NSFHGRTLFTVNVGGQPKYSDGFGPKFEGI------THVPY---------NDLEALKAAI 183 + +HG T ++V G F G+ P N +E L + Sbjct: 144 SGYHGDTFGAMSVCDP---DTGMHSLFTGMLAEQLFAEAPQCGFDAAWNENGIEDLHQKL 200 Query: 184 S---DKTCAVVLEPI-QGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELF 239 + AV++EP+ QG GG+ YL R+LCDE+ LL+FDE+ +G GR G++F Sbjct: 201 RQHHEAVAAVIIEPVVQGAGGMRFYSPHYLIRLRELCDEYGVLLIFDEIATGFGRTGKMF 260 Query: 240 AYMHYGVVPDILSSAKSLGGGF-PIGAMLTTGEIAKHLS-----VGTHGTTYGGNPLASA 293 A H GVVPDI+ K+L GG+ + A L +A +S + HG T+ NPLA + Sbjct: 261 ALEHAGVVPDIMCVGKALTGGYMTLAATLAADHVADTISSAEPGLFMHGPTFMANPLACS 320 Query: 294 VAEAALDVI 302 VA A++D++ Sbjct: 321 VASASIDLL 329 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: 396 Number of extensions: 23 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: 2 Length of query: 406 Length of database: 428 Length adjustment: 31 Effective length of query: 375 Effective length of database: 397 Effective search space: 148875 Effective search space used: 148875 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 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