Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_090442706.1 BLS63_RS08505 aspartate aminotransferase family protein
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_900100495.1:WP_090442706.1 Length = 460 Score = 171 bits (433), Expect = 4e-47 Identities = 125/414 (30%), Positives = 204/414 (49%), Gaps = 42/414 (10%) Query: 27 IPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHVSNVF-TNEP 85 + VRGEG +WD G+ +D G+ T+LG+ LV A T Q +++ + + F T P Sbjct: 39 VMVRGEGLHLWDNDGKRYLDGMSGLWCTNLGYGRQDLVAAATRQMEQLPYYNMFFHTTHP 98 Query: 86 AL----RLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNSF 141 A+ L+ ++ ++ NSG+EANE + RRY + PQK +I N + Sbjct: 99 AVVELSETLFSLLPGHYSHAIY-TNSGSEANEVLIRTVRRYWQILGQPQKKVMIGRWNGY 157 Query: 142 HGRTLFTVNVGGQPKYSDGFGPKFEGITHVP----YNDLEALKAAISDKTCAVVLE---- 193 HG TL +GG K+ G I H+ Y L A + CA+ LE Sbjct: 158 HGSTLAATALGGM-KFMHEMGGMLPDIAHIDEPYWYAHGGELSPAEFGRRCALQLEEKIL 216 Query: 194 -------------PIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFA 240 P QG GG++ ++Y +++C +++ LL DEV G GR GE FA Sbjct: 217 ELGAENVAGFIAEPFQGAGGMIFPPESYWPEIQRICRQYDVLLCADEVIGGFGRTGEWFA 276 Query: 241 YMHYGVVPDILSSAKSLGGGF-PIGAMLTTGEIAKHL----SVGTHGTTYGGNPLASAVA 295 + H+G PD LS AK L G+ P+G ++ + IA+ L V HG TY G+P+A+AVA Sbjct: 277 HQHFGFQPDTLSIAKGLTSGYVPMGGLVLSKRIAEMLVEQGGVFAHGLTYSGHPVAAAVA 336 Query: 296 EAALDVINTPEVLDGVKAKHERFKSR-LQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKA 354 A + + V+ VK + + L+++ E+ + +I+G GL+ ++ + Sbjct: 337 LANIKALRDEGVVSRVKDDTGPYLQQCLRQVFGEHPLVGDIQGSGLVAALQFAEDKSSRK 396 Query: 355 R-----DV---LNAAEKEAVMVLQASPDVVRFAPSLVIDDAEIDEGLERFERAV 400 R D+ + E ++++++ + AP+LV A++DE LE+ +RAV Sbjct: 397 RFANENDIAWRCRSIGFEEGLIIRSTLGRMIMAPALVASHADLDELLEKTKRAV 450 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: 516 Number of extensions: 30 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: 460 Length adjustment: 32 Effective length of query: 374 Effective length of database: 428 Effective search space: 160072 Effective search space used: 160072 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