Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_011384093.1 AMB_RS08515 aspartate aminotransferase family protein
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_000009985.1:WP_011384093.1 Length = 459 Score = 166 bits (421), Expect = 1e-45 Identities = 129/415 (31%), Positives = 205/415 (49%), Gaps = 47/415 (11%) Query: 30 RGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRI--WHVSNVFTNEPAL 87 RG+G RV+D++GR+ I+ G+ TSLG LV+A Q +++ +H+ + T++ + Sbjct: 38 RGQGVRVYDEAGRDYIEGLAGLWCTSLGWGEERLVEAAARQMRQLPFYHLFSHKTHDVGV 97 Query: 88 RLARKLVDATFA--ERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNSFHGRT 145 L +L+ +VFLA SG+EAN+ A KL AN + P K +IIA ++HG T Sbjct: 98 ELCARLLAMAPVPMSKVFLAGSGSEANDTAIKLIHYRANALGTPDKKKIIAREKAYHGVT 157 Query: 146 LFTVNVGGQPKYSDGFGPKFEGITHV--PYN-------------------DLEALKAAIS 184 + T ++ G F G+ P++ +LEA+ A Sbjct: 158 VATASLTGLVNNQRSFDLPIPGVLRAACPHHYRFAKDGESEEDFSTRLAGELEAMILAEG 217 Query: 185 -DKTCAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMH 243 D A EP+ G GGV+ Y + + D ++ LLV DEV G GR G++F Sbjct: 218 PDTVAAFFAEPVMGAGGVIVPPAGYFPKIQAVLDRYDVLLVVDEVICGFGRTGKMFGTET 277 Query: 244 YGVVPDILSSAKSLGGGF-PIGAMLTT----GEIAK---HLSVGTHGTTYGGNPLASAVA 295 +G+ PD+++ AK L G+ PI A++ G +A+ + V HG TYGG+P+++AVA Sbjct: 278 FGIRPDMMTLAKGLSSGYAPISALMVNERVYGPVAEESGRIGVFGHGYTYGGHPVSAAVA 337 Query: 296 EAALDVINTPEVLDGVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGK-- 353 L++ ++L V + L+ + + + + E RG+GL+ L + + Sbjct: 338 LETLNIYAERDILAQVAEVGPVLQDGLRAL-RGHPLVGEARGVGLIGAVELVADKANRAP 396 Query: 354 --------ARDVLNAAEKEAVMVLQASPDVVRFAPSLVIDDAEIDEGLERFERAV 400 AR V A K ++L+A D V FAP LVI A+I E L RF A+ Sbjct: 397 FPPELAVGARVVAKAQAKG--VILRAMGDAVAFAPPLVISKADIAEMLRRFGLAL 449 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: 479 Number of extensions: 29 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: 459 Length adjustment: 32 Effective length of query: 374 Effective length of database: 427 Effective search space: 159698 Effective search space used: 159698 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 17 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