Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_011159270.1 TX73_RS19050 aspartate aminotransferase family protein
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_000195775.1:WP_011159270.1 Length = 463 Score = 178 bits (452), Expect = 3e-49 Identities = 108/323 (33%), Positives = 173/323 (53%), Gaps = 16/323 (4%) Query: 30 RGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQR-IWHVSNVFTNEPALR 88 +G G ++D+ G +D G V +LG HP + KAL + ++ + + A Sbjct: 46 KGTGQYLYDRDGARYLDLLSGFGVFALGRNHPVVRKALQSVLDADLPNLVQLDVSTLAGI 105 Query: 89 LARKLVDAT-FAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNSFHGRTLF 147 LA +L++ + ++VF ANSGAE+ EAA K AR + I+ +S+HG T Sbjct: 106 LAERLLEQVPYLDKVFFANSGAESVEAAIKFARGATG------RNGIVNCDHSYHGLTYG 159 Query: 148 TVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDK-TCAVVLEPIQGEGGVLPAQQ 206 +++ + GFGP G+T +P+NDLEAL+ +S + A ++EPIQG+G +P + Sbjct: 160 ALSLTDDQNFQGGFGPLLPGVTTIPFNDLEALEKVLSTREVAAFIVEPIQGKGVNMPTDE 219 Query: 207 AYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKSLGGG-FPIGA 265 +L GA LC + L V DE+Q+GMGR G A H+ V PD++ +K+L GG P+GA Sbjct: 220 -FLPGAAALCKRYGTLFVADEIQTGMGRTGRFLAVEHWNVEPDMVLLSKALSGGHVPVGA 278 Query: 266 MLTTGEIAKHL-----SVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKHERFKS 320 +LT I + HG+T+ N LA A A L+V+ ++++ + + Sbjct: 279 VLTRKSIFDKIFNRMDRAVVHGSTFAKNDLAMAAGIATLEVLKAEKLVEAAAKRGAELRL 338 Query: 321 RLQKIGQEYGIFDEIRGMGLLIG 343 L ++ Y + E+RG GL+IG Sbjct: 339 ALTRMVPGYELLKEVRGKGLMIG 361 Lambda K H 0.318 0.135 0.394 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: 420 Number of extensions: 17 Number of successful extensions: 5 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: 406 Length of database: 463 Length adjustment: 32 Effective length of query: 374 Effective length of database: 431 Effective search space: 161194 Effective search space used: 161194 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: 51 (24.3 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