Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate WP_011033683.1 MM_RS09040 aspartate aminotransferase family protein
Query= SwissProt::Q8ZPV2 (408 letters) >NCBI__GCF_000007065.1:WP_011033683.1 Length = 424 Score = 134 bits (338), Expect = 4e-36 Identities = 91/295 (30%), Positives = 143/295 (48%), Gaps = 23/295 (7%) Query: 20 PAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIGNGYT 79 P PF GS++ D G EYID+ LGH HP ++EA+ +Q +R W G Sbjct: 34 PYPFYTASANGSKIRDLDGNEYIDYCLAYGPAILGHNHPVIKEAIRQQLDRGWLYGT--P 91 Query: 80 NEPALRLAKKLID-ATFAERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAF 138 E + LA+K+ + + F ++G EA +AL+LAR + ++ + + F Sbjct: 92 TELEVTLAEKVASYYPSIDMLRFVSTGTEATMSALRLARGF------TRRNKFIKIEGGF 145 Query: 139 HG---RTLFTVSAGGQPTYSQDFAPLPPDIR----HAAYNDLNSASALID---DNTCAVI 188 HG L +G D +P D A YND+ + ++L++ D+ AVI Sbjct: 146 HGAHDAVLVKAGSGATTLGEPDSLGIPADFTKHTLQAPYNDIETMTSLVEKNRDDLAAVI 205 Query: 189 VEPVQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPDIL 248 +EPV G G + +L+ LR+L + + LLIFDEV TG R A ++GV PD+ Sbjct: 206 IEPVLGNIGPVLPLPGYLEELRKLTEENDVLLIFDEVITGF-RLAMGGAQEYFGVVPDMT 264 Query: 249 TTAKALGGGFPIGAMLTTQDYASVMTPG---THGTTYGGNPLATAVAGKVLDIIN 300 T K +GGG PIG ++ ++ P T+ G+P + A ++D +N Sbjct: 265 TLGKIVGGGLPIGVFGGKREIMEMIAPSGAVYQAGTFSGSPCSVAAGIAMVDYLN 319 Lambda K H 0.320 0.137 0.413 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: 433 Number of extensions: 31 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: 408 Length of database: 424 Length adjustment: 31 Effective length of query: 377 Effective length of database: 393 Effective search space: 148161 Effective search space used: 148161 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 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