Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_014518834.1 CA_RS02090 aspartate aminotransferase family protein
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >NCBI__GCF_000008765.1:WP_014518834.1 Length = 426 Score = 228 bits (580), Expect = 3e-64 Identities = 141/409 (34%), Positives = 218/409 (53%), Gaps = 42/409 (10%) Query: 26 VRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTGNGYTN-EPVL 84 VRGEG+ L+ + G++ +DFA G+AV LGH +P ++KA EQ K H G+ E + Sbjct: 25 VRGEGAYLYTEDGRKVLDFASGVAVCNLGHNNPAVIKAAKEQMDKLIHGGHNVVYYESYV 84 Query: 85 RLAKQLIDATF-ADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRTL 143 +LA+++++ T V+F NSGAEANE A+KLA+ + +++ I++FK +FHGRTL Sbjct: 85 KLAEKIVELTGNKTMVYFSNSGAEANEGAIKLAK------YITKRQAIISFKGSFHGRTL 138 Query: 144 FTVS-AGGQPAYSQDFAPLPPQIQHAIYNDL---------------------DSAKALID 181 T S G Y +++ L P + A Y D K LI+ Sbjct: 139 ATTSITGSSSKYRKNYEGLLPSVYFAEYPYCFRCPYKQNKESCNMECISQFEDMFKKLIE 198 Query: 182 -DNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMH 240 ++ A+I+EP+QGEGG + FL+ +RE+CD + LIFDEVQ G GRTG+++A+ + Sbjct: 199 PESVAAIIMEPVQGEGGYIVPPKKFLKAVREICDKYGICLIFDEVQCGFGRTGKIFAHEN 258 Query: 241 YGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATIN 300 + V PD+ + AKA+ GFP+ A++ + G HG T+GGNP+ACA + ATI Sbjct: 259 FEVEPDIFTCAKAIASGFPLSAVIGKKELMEKWPAGAHGGTFGGNPVACAAS---LATIK 315 Query: 301 TRE--VLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIG---CVLKDEYAGKAKAIS 355 E VL+ + E L + +Y +IRG+GL+IG C + G Sbjct: 316 ELESGVLDNANNMGNYLKEELLKLKDKYACIGDIRGIGLMIGMEFCKENNNPDGDIVTFI 375 Query: 356 NQAAEEGLMILIAGA---NVVRFAPALIISEDEVNSGLDRFELACKRFL 401 + A +IL+ NV+RF L + + E++ + E +L Sbjct: 376 REVAVNNNLILLGCGTEHNVLRFIAPLTVEKSEIDMAISIVEKGIVEYL 424 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: 463 Number of extensions: 21 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: 426 Length adjustment: 31 Effective length of query: 375 Effective length of database: 395 Effective search space: 148125 Effective search space used: 148125 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