Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_108401693.1 B9Z44_RS03080 aspartate aminotransferase family protein
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_003063475.1:WP_108401693.1 Length = 398 Score = 259 bits (661), Expect = 1e-73 Identities = 151/364 (41%), Positives = 204/364 (56%), Gaps = 9/364 (2%) Query: 31 GEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHVSNVFTNEPALRLA 90 G G RVWD +G+ +D GIAV +LGHAHP L AL +Q ++ H N + LA Sbjct: 24 GRGLRVWDTNGKAYLDALAGIAVNTLGHAHPQLTPALQDQVGKMIHSCNYYHIPLQEALA 83 Query: 91 RKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNSFHGRTLFTVN 150 KLV+ + F NSG EANEAA KLAR++ + + G +K EI+ +FHGR+L T+ Sbjct: 84 AKLVELSGMTNAFFCNSGLEANEAAIKLARKFGH-MKGIEKPEIVVYEKAFHGRSLATLA 142 Query: 151 VGGQPKYSDGFGPKFEGITHVPYNDLEALKAAI--SDKTCAVVLEPIQGEGGVLPAQQAY 208 G K +GFGP EG VP N++EALK A + AV E IQGEGGV P Y Sbjct: 143 ATGNEKIKEGFGPMMEGYIRVPVNNIEALKKATEGNPNVAAVFFETIQGEGGVKPMNTDY 202 Query: 209 LEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKSLGGGFPIGAMLT 268 L+ R+LCD+ + LL+ DEVQ GMGR G+ FA+ G+VPD++ AK LG G P+GA++ Sbjct: 203 LQQVRQLCDKRDWLLMIDEVQCGMGRTGKWFAHQWSGIVPDVMPLAKGLGSGVPVGAVVA 262 Query: 269 TGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKHERFKSRLQKIGQE 328 + A G HGTT+GGNPLA + ++ ++LD V + L + Sbjct: 263 GPKAAHIFQPGNHGTTFGGNPLAMRAGVETIRIMEEDKLLDNVLKVGAHLHAALHRELDG 322 Query: 329 YGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASPD-VVRFAPSLVIDDA 387 EIRG GL+IG L + VL +A ++L + D VVR P L+I +A Sbjct: 323 VKGVKEIRGQGLMIGIDL-----DRPCGVLMQRALDAGLLLSVTADSVVRLVPPLIITEA 377 Query: 388 EIDE 391 E DE Sbjct: 378 EADE 381 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: 383 Number of extensions: 20 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: 398 Length adjustment: 31 Effective length of query: 375 Effective length of database: 367 Effective search space: 137625 Effective search space used: 137625 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