Align N-succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate WP_101442815.1 BD749_RS02630 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= reanno::Btheta:353284 (373 letters) >NCBI__GCF_002846395.1:WP_101442815.1 Length = 383 Score = 453 bits (1165), Expect = e-132 Identities = 223/376 (59%), Positives = 286/376 (76%), Gaps = 3/376 (0%) Query: 1 MKLFDVYPLYDINIVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATL 60 M LFDVYPL+DI V+ G VWD+ G +YLDLYGGHAVISIGH+HPHYV+ I+ Q+ + Sbjct: 1 MNLFDVYPLFDIEPVRAAGLSVWDKEGRKYLDLYGGHAVISIGHSHPHYVKRIARQLYDI 60 Query: 61 GFYSNSVINKLQQQVAERLGKISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFS 120 GFYSN+V +QQ++A +LGK+SGY+ YS FL NSGAEANENALKLASF GR KVISFS Sbjct: 61 GFYSNAVQMPMQQELAVKLGKLSGYDAYSFFLCNSGAEANENALKLASFQTGRKKVISFS 120 Query: 121 KAFHGRTSLAVEATNNPTIIAPINNNGHVTYLPLNDIEAMKQELAKG--DVCAVIIEGIQ 178 +FHGRTS AV AT++ +I+APIN ++ ++P ND+ A ++ L K ++ AVI+EGIQ Sbjct: 121 ASFHGRTSAAVAATDDTSIVAPINQTDNIIFMPFNDVAAFEEALQKHGQELAAVIVEGIQ 180 Query: 179 GVGGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITVAKG 238 GVGG+ IPT F++ L C + G +LILDE+QSGYGRSGKFFAHQ+ IQPD+ITVAKG Sbjct: 181 GVGGVNIPTVNFLKALEAGCKKVGALLILDEVQSGYGRSGKFFAHQHAGIQPDLITVAKG 240 Query: 239 IGNGFPMAGVLISPMFKPVYGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKAVGDYL 298 +GNGFP+ GVLISP + +G LGTTFGGN+LAC+A+LAV++VIE++ L+ENA +G YL Sbjct: 241 MGNGFPVGGVLISPEIEARHGMLGTTFGGNYLACAASLAVLEVIEKEELLENATIMGHYL 300 Query: 299 LEELKKFPQIKEVRGRGLMIGLEFEEPIKELRSRLIYDEHVFTGASGT-NVLRLLPPLCL 357 E+L+ P +KEVRG+GLMIG+E EP +R L+ +FTG+S N LRLLP L + Sbjct: 301 KEQLEGMPGVKEVRGQGLMIGIELNEPCAGIRKELLSQFGIFTGSSSNKNTLRLLPALTI 360 Query: 358 SMEEADEFLARFKRVL 373 S EAD FL F +L Sbjct: 361 SKAEADLFLKAFSSIL 376 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: 411 Number of extensions: 16 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: 373 Length of database: 383 Length adjustment: 30 Effective length of query: 343 Effective length of database: 353 Effective search space: 121079 Effective search space used: 121079 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