Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_002968535.1 BIBO1_RS18510 aspartate aminotransferase family protein
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_000182725.1:WP_002968535.1 Length = 484 Score = 181 bits (460), Expect = 3e-50 Identities = 126/415 (30%), Positives = 207/415 (49%), Gaps = 44/415 (10%) Query: 30 RGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWH-VSNVFTNEPALR 88 R EG +DQ+GR ++DF GG + GH HP ++ A + + + H ++ F ++ A Sbjct: 67 RAEGMYYYDQNGRRILDFFGGFGSLAFGHNHPRIIAARRKFQEELRHEIAIAFMSQYAAA 126 Query: 89 LARKLVDATFAE--RVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNSFHGRTL 146 LA L + + VFL +SG+EA EAA K+A R A GP+K +I+ A NSFHG+T Sbjct: 127 LAYDLAACSPGDLDMVFLGSSGSEAMEAAIKVAERAA----GPKKPKIVYAENSFHGKTK 182 Query: 147 FTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISD--KTCAVVLEPIQGEGGVLPA 204 +++ Y F + VP+ D+ A++ A + +VLE +QG GG++ A Sbjct: 183 GVLSITDGGLYRGEF-KLVDNTVRVPFGDITAIENAFRSDPEIGTIVLETVQGGGGIIQA 241 Query: 205 QQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKSLGGGFPIG 264 + + R+LCD + + V DEVQ G GR G+ +A+ HYGV+PD+ + AKSLGGG Sbjct: 242 DAEFWQKLRQLCDRYGVIWVADEVQCGFGRTGKFYAFEHYGVIPDVTALAKSLGGGKAAM 301 Query: 265 AMLTTGEIAKHLSVGTHGT-------TYGGNPLASAVAEAALDVINTPEVLDGVKAKHER 317 A + + GT T T+GG A A A++++ +++D + Sbjct: 302 AAMIARRDIYMKAYGTPKTAMIHAMATFGGIGEACITAIEAVNILYDEQLIDNSAEVGDY 361 Query: 318 FKSRLQKIGQEY-GIFDEIRGMGLLIG------------------AALTDEWKGKARDVL 358 RL+++ Y G+ ++RG G+++G A L D+ KG + Sbjct: 362 LLERLKELQVRYPGLLKDVRGKGMMVGLEFHDFSQAMPMVLRPMLAMLDDKLKGSLPGFI 421 Query: 359 NA--AEKEAVMV--LQASPDVVRFAPSLVIDDAEIDEGL----ERFERAVAKLVR 405 + V+V + + +V+R P L+ A +DE + E R + K+V+ Sbjct: 422 GSHLLRDHGVLVAFTEYNRNVIRLEPPLICQRAHVDEFIKALDEVLSRGIVKIVK 476 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: 483 Number of extensions: 20 Number of successful extensions: 6 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: 484 Length adjustment: 32 Effective length of query: 374 Effective length of database: 452 Effective search space: 169048 Effective search space used: 169048 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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