Align N-succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate WP_028489358.1 Q394_RS0111125 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= reanno::Cola:Echvi_3848 (381 letters) >NCBI__GCF_000621325.1:WP_028489358.1 Length = 436 Score = 114 bits (286), Expect = 4e-30 Identities = 132/422 (31%), Positives = 192/422 (45%), Gaps = 69/422 (16%) Query: 11 DVTPV-KASGSTIWDDQGNEYLDLYGGHAVISIGHSHPHYTKRIKEQ---LDNIAFYSNS 66 D P+ A G ++ + G E+LDL V GH+HP I +Q L+ + F + Sbjct: 23 DAIPITSAKGIHLYAEDGREFLDLISSWWVNLHGHAHPTIAAAIAKQAHTLEQVIFAGFT 82 Query: 67 VQIPIQKELATKLGQLSGYPDYDLFLCNSGAEANENALKLA------SFETGKKGFIAFT 120 Q Q LA +L Q +F + G+ A E ALK+A E + F+AF Sbjct: 83 HQPAAQ--LAHELVQRLPKGLNRVFFSDDGSTAVEVALKMALQYWRNHGEGQRTRFLAFE 140 Query: 121 KGFHGRTSGAVALTDNPKIIAPFNAHEG----VHILPF-----NDLEAVEKQLAT----- 166 G+HG T GA++ FN + V +LPF D E K+ A Sbjct: 141 GGYHGDTVGAMSAGKGSGF---FNTYGSLLFEVGLLPFPETWDGDTEVEAKEQAALVRLD 197 Query: 167 -------GTIAGVIVEG-IQGVGGIQVPDPAFLLGLSALTKQYGAKLILDEVQSGYARSG 218 T+A VI+E IQG G+++ P FL L+A + G LI DEV +G+ R+G Sbjct: 198 EYLAAHGNTLAAVIMEPLIQGSSGMRMCRPEFLQALAARLRAAGILLIFDEVMTGFGRTG 257 Query: 219 KFFAHQWVEGLKPDLITVAKGMGNGFPIGGVLISPE--FKASHG-------LLGTTFGGN 269 FA + + PD+I ++KG+ GF V ++ E + A G + G +F N Sbjct: 258 AMFASLKAQ-VTPDIICLSKGLTAGFLPMSVTVATEAIYAAFLGDSFDRALVHGHSFTAN 316 Query: 270 HLACAAALAVLEVIDEEN------LITAAAENGKAIMAALEKVAGVTEVRGKGLMIGFDL 323 L CAAALA L+V ++E LI A G A +AA V VR G + FD+ Sbjct: 317 PLGCAAALASLQVFEDEQTLAKLPLIEAWHRQGLATLAAHPM---VQRVRVMGTIAAFDV 373 Query: 324 A-TEAG---PVRA---ALIHEHKIFTGSAGGKHTIRLLPPLNIEP----KALTLFLEKLE 372 A +AG P+ A A HE + G + + LLPP I +A ++ L LE Sbjct: 374 AVADAGYTSPIGAYLKAFFHERGLLLRPLG--NVVYLLPPYCINEQELVQAYSVILSALE 431 Query: 373 TV 374 ++ Sbjct: 432 SL 433 Lambda K H 0.318 0.137 0.400 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: 426 Number of extensions: 22 Number of successful extensions: 4 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: 381 Length of database: 436 Length adjustment: 31 Effective length of query: 350 Effective length of database: 405 Effective search space: 141750 Effective search space used: 141750 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