Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_008507916.1 BIBO1_RS13055 aspartate aminotransferase family protein
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_000182725.1:WP_008507916.1 Length = 403 Score = 324 bits (830), Expect = 3e-93 Identities = 175/384 (45%), Positives = 234/384 (60%), Gaps = 5/384 (1%) Query: 21 YAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHVSNV 80 Y AA RGEG + + G IDFA GIAV SLGH+HP LV+ L QA+++WH+SN+ Sbjct: 14 YNRAALRFERGEGIWLITEDGERYIDFAAGIAVNSLGHSHPHLVETLKTQAEKLWHLSNI 73 Query: 81 FTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNS 140 + +L R+LV+ TFA++VF NSGAEA E A K ARRY P+++ II + Sbjct: 74 YEIPAQEKLGRRLVENTFADKVFFTNSGAEALECAIKTARRYQYVSGHPERFRIITFEGA 133 Query: 141 FHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKTCAVVLEPIQGEGG 200 FHGRTL T+ GGQ KY +GFGPK EG VP+ D AL+AAI+ +T ++LEPIQGEGG Sbjct: 134 FHGRTLATIAAGGQAKYLEGFGPKVEGFDQVPFGDEAALRAAITPETAGILLEPIQGEGG 193 Query: 201 VLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKSLGGG 260 + + +L R++CDE+ LL+ DEVQ+G+GR G+ FA+ G+ PDI++ AK +GGG Sbjct: 194 LRAFPEEFLRLVRQICDENGLLLLLDEVQTGVGRTGKFFAHEWAGIRPDIMAIAKGIGGG 253 Query: 261 FPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKHERFKS 320 FPIGA L T E AK ++ G HGTTYGGNPL AV A LDV+ ++ V+A K Sbjct: 254 FPIGACLATAEAAKGMTAGMHGTTYGGNPLGMAVGNAVLDVVLADGFMENVQATALVMKQ 313 Query: 321 RLQKIGQEY-GIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASPDVVRFA 379 L + Y + EIRG GLL+G ++ A E V+ + A +VVR Sbjct: 314 GLASLVDRYPNVVSEIRGRGLLMGLKCV----VPNTSLIQALRDEHVLSVGAGDNVVRLL 369 Query: 380 PSLVIDDAEIDEGLERFERAVAKL 403 P L+ E E L+ E AV +L Sbjct: 370 PPLITTPEEAREALKHIETAVERL 393 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: 453 Number of extensions: 23 Number of successful extensions: 2 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: 403 Length adjustment: 31 Effective length of query: 375 Effective length of database: 372 Effective search space: 139500 Effective search space used: 139500 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: 50 (23.9 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