Align N-succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate WP_055434904.1 ASC41_RS01645 aspartate aminotransferase family protein
Query= reanno::Btheta:353284 (373 letters) >NCBI__GCF_001418085.1:WP_055434904.1 Length = 376 Score = 431 bits (1108), Expect = e-125 Identities = 216/374 (57%), Positives = 275/374 (73%), Gaps = 1/374 (0%) Query: 1 MKLFDVYPLYDINIVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATL 60 M LF+VYPL+DI VK V+DEN T+YLDLYGGHAVISIGH+HP YV IS+QVA L Sbjct: 1 MSLFNVYPLFDITPVKAVDVFVYDENETKYLDLYGGHAVISIGHSHPKYVAAISDQVAKL 60 Query: 61 GFYSNSVINKLQQQVAERLGKISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFS 120 GFYSNS+ N LQ Q+A +L ++SG +DY LFL NSGAEANENALKLASF+NG+ K+I+F Sbjct: 61 GFYSNSIQNPLQVQLANKLEQLSGCKDYELFLCNSGAEANENALKLASFHNGKKKIIAFK 120 Query: 121 KAFHGRTSLAVEATNNPTIIAPINNNGHVTYLPLNDIEAMKQELAKGDVCAVIIEGIQGV 180 FHGRTS AV AT+N IIAPIN V L L D++ +++ LAK DVCAVIIE IQGV Sbjct: 121 NGFHGRTSAAVAATDNAKIIAPINAQQEVEILELGDLKGVEKALAKNDVCAVIIECIQGV 180 Query: 181 GGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITVAKGIG 240 GG+ TTEF + L ++C + T I DE+QSG+GR+G FFA Q ++ PDII++AKG+G Sbjct: 181 GGLDESTTEFYEGLDELCEKYNTCFIADEVQSGFGRTGDFFAFQKYNVMPDIISIAKGMG 240 Query: 241 NGFPMAGVLISPMFKPVYGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKAVGDYLLE 300 NGFP+ G+LI P K +G LGTTFGGNHLAC A+ V++VI+++NL++NAK + Y +E Sbjct: 241 NGFPIGGILIHPNIKASFGLLGTTFGGNHLACVASSTVLEVIKEENLMQNAKDISAYFVE 300 Query: 301 ELKKFPQIKEVRGRGLMIGLEFEEPIKELRSRLIYDEHVFTG-ASGTNVLRLLPPLCLSM 359 + K IK ++GRGLM+GLEF+ PI ELR +LI+D +FTG A N+LR+LPPL + Sbjct: 301 KAKGISAIKNIKGRGLMLGLEFDFPIAELRKKLIFDHKIFTGSAKNPNLLRILPPLTIKK 360 Query: 360 EEADEFLARFKRVL 373 E D F K L Sbjct: 361 EHVDLFFEALKSEL 374 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: 406 Number of extensions: 12 Number of successful extensions: 2 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: 376 Length adjustment: 30 Effective length of query: 343 Effective length of database: 346 Effective search space: 118678 Effective search space used: 118678 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 26 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