Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_012976449.1 AZL_RS20880 aspartate aminotransferase family protein
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_000010725.1:WP_012976449.1 Length = 473 Score = 134 bits (338), Expect = 4e-36 Identities = 111/358 (31%), Positives = 170/358 (47%), Gaps = 32/358 (8%) Query: 30 RGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHVSNVFTNEPALRL 89 RG GSRV D G E ID+ G+ LGH PA+ KA+ + ++ V + + + + L Sbjct: 75 RGTGSRVTDVDGNEYIDYLLGLGPMLLGHRPPAVTKAVVDCIEQRGTVFALPSADETI-L 133 Query: 90 ARKLVDATFA-ERVFLANSGAEANEAAFKLARRY----------------ANDVYGPQKY 132 ARK+ A ERV L N+G EA +LAR + ++ VY + Sbjct: 134 ARKITAAVPGLERVRLCNTGTEAVLYTVRLARAFTGRPKLIRFEGMYHGFSDGVYWSKHP 193 Query: 133 EIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAIS---DKTCA 189 ++ AA GR V P G G + + +P+ND+EAL+ + D+ A Sbjct: 194 KLDAA-----GRDDAPTAVPQGPGMPRGVG---DSLIILPWNDVEALRTTLEREGDQIAA 245 Query: 190 VVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPD 249 V+ EPI G + + YLE R+L +H L++ DEV +G R+ A HYGV PD Sbjct: 246 VLSEPIMCNTGCILPEPGYLEAMRELTRKHGVLMILDEVITGF-RIALGGAQAHYGVTPD 304 Query: 250 ILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGT--TYGGNPLASAVAEAALDVINTPEV 307 + AK LGGGFP+ AM +I + GT TY N +A + A A LD + P + Sbjct: 305 LSVFAKGLGGGFPVAAMGGRADIMALVENGTVSIAGTYNANMIAVSAANATLDELAQPGM 364 Query: 308 LDGVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEA 365 + + A +R + L ++ ++ I + G+G + D RD + A+ +A Sbjct: 365 YERLYAVSDRLREGLDRLIRDLRIPAHVVGLGPVFQLWFADRPIRNYRDAVRHADHDA 422 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: 494 Number of extensions: 21 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: 473 Length adjustment: 32 Effective length of query: 374 Effective length of database: 441 Effective search space: 164934 Effective search space used: 164934 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