Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_089302612.1 CHB84_RS16910 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >NCBI__GCF_900188115.1:WP_089302612.1 Length = 422 Score = 228 bits (582), Expect = 2e-64 Identities = 149/395 (37%), Positives = 206/395 (52%), Gaps = 40/395 (10%) Query: 28 GEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTGNGYT---NEPVL 84 GEG L+D G+ ++DF GI V + GH HP++V A EQ GK H YT ++P+ Sbjct: 19 GEGVYLYDHSGRRHLDFTAGIGVTSTGHCHPKVVAAAQEQVGKLIH--GQYTTVMHDPLR 76 Query: 85 RLAKQLIDAT--FADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRT 142 LA++L D D VFF NSG+EA EAAL+LAR+ + + I+ F+ FHGRT Sbjct: 77 SLAERLGDVLPPGLDSVFFANSGSEAVEAALRLARQ------ATGRPNIIVFQGGFHGRT 130 Query: 143 LFTVS-AGGQPAYSQDFAPLPPQIQHAIY------------------NDLDSAKALID-- 181 + S + +APL + A + +LD A + Sbjct: 131 VGAASLTTSGTRFRAGYAPLMDGVHVAPFPFAYRYGWDEATATRFALQELDYLFATMSPG 190 Query: 182 DNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHY 241 + T A+ VEP+ GEGG VPA+ +FL GLRE D H LL+ DEVQTG GRTG+ + H+ Sbjct: 191 EETAAIFVEPVLGEGGYVPANREFLAGLRERADKHGILLVADEVQTGFGRTGKFWGMEHF 250 Query: 242 GVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINT 301 V PD++ TAK L GFP+ + AS G+ G TYGGN +ACA A I Sbjct: 251 DVQPDVVITAKGLASGFPLSGIAASTELMGKAWPGSQGGTYGGNAVACAAALATLDVIQE 310 Query: 302 REVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGC--VLKDEYA--GKAKAISNQ 357 ++N + E I ++ ++RGLGL++G V D A AKA Sbjct: 311 EGLVNNAATQGARLLEGSRQIAEKFPQIGDVRGLGLMVGSEFVTADGRADPDTAKAAQQA 370 Query: 358 AAEEGLMILIAGA--NVVRFAPALIISEDEVNSGL 390 AAE GL++L+ GA N VR PAL++S +V+ L Sbjct: 371 AAERGLLLLMCGAWMNTVRMIPALVVSGAQVDDAL 405 Lambda K H 0.321 0.137 0.412 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: 428 Number of extensions: 23 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: 422 Length adjustment: 31 Effective length of query: 375 Effective length of database: 391 Effective search space: 146625 Effective search space used: 146625 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 Jul 25 2024. The underlying query database was built on Jul 25 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