Align N-succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate WP_066329149.1 BLR17_RS14830 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= reanno::Btheta:353284 (373 letters) >NCBI__GCF_900100165.1:WP_066329149.1 Length = 379 Score = 440 bits (1132), Expect = e-128 Identities = 215/374 (57%), Positives = 274/374 (73%), Gaps = 1/374 (0%) Query: 1 MKLFDVYPLYDINIVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATL 60 M LFDVYPLY I VK C ++DE GTEYLDLY GH VISIGH P YV + Q+ L Sbjct: 1 MNLFDVYPLYPITPVKAVDCTIYDEKGTEYLDLYSGHGVISIGHTQPDYVAKVKEQLDNL 60 Query: 61 GFYSNSVINKLQQQVAERLGKISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFS 120 FYSN++ N LQ ++AE+LGK SG D+SLFL +SGAEANENALKLASF+ +++VI+F Sbjct: 61 SFYSNAIQNPLQVELAEKLGKASGLTDFSLFLCSSGAEANENALKLASFHTNKSRVIAFD 120 Query: 121 KAFHGRTSLAVEATNNPTIIAPINNNGHVTYLPLNDIEAMKQELAKGDVCAVIIEGIQGV 180 +FHGRTS AV T+N I+AP+N VT+LPLN IE ++ EL KGDVCAVIIE IQGV Sbjct: 121 NSFHGRTSAAVAVTDNKKIVAPLNAQQEVTFLPLNQIELVEAELKKGDVCAVIIEPIQGV 180 Query: 181 GGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITVAKGIG 240 GG+ TTEF Q L K ILILDE+QSGYGRSGKFFA Q++ I PDI+T AKG+G Sbjct: 181 GGLDQGTTEFFQALEKASKANDVILILDEVQSGYGRSGKFFAFQHHGINPDIVTTAKGMG 240 Query: 241 NGFPMAGVLISPMFKPVYGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKAVGDYLLE 300 NGFP+ GVLISP F+ YG LGTTFGG+HLAC+A +AV+DV+E L+EN V +Y E Sbjct: 241 NGFPIGGVLISPKFQASYGLLGTTFGGSHLACAAGIAVLDVMEDKKLIENTNKVSEYFFE 300 Query: 301 ELKKFPQIKEVRGRGLMIGLEFEEPIKELRSRLIYDEHVFT-GASGTNVLRLLPPLCLSM 359 +K P+IK+V+GRGLM+G+EF+ + LR ++I ++++FT GA+ N+LR+LPPL ++ Sbjct: 301 AIKVIPEIKKVKGRGLMLGVEFDFDVSALRKKMIIEKYIFTGGANNKNLLRILPPLTITT 360 Query: 360 EEADEFLARFKRVL 373 E D F+ + L Sbjct: 361 EAIDTFIVALQESL 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: 427 Number of extensions: 19 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: 379 Length adjustment: 30 Effective length of query: 343 Effective length of database: 349 Effective search space: 119707 Effective search space used: 119707 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