Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_013450865.1 CALNI_RS03705 aspartate aminotransferase family protein
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_000183405.1:WP_013450865.1 Length = 386 Score = 317 bits (811), Expect = 5e-91 Identities = 163/374 (43%), Positives = 240/374 (64%), Gaps = 5/374 (1%) Query: 29 VRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHVSNVFTNEPALR 88 V+G+ ++D++G++ +DFA GIAVT+LGH++ + + + Q+ + H SN++ N Sbjct: 16 VKGDYFYLFDENGKKYVDFATGIAVTNLGHSNKEIAEIICRQSATLMHTSNLYKNPIQEE 75 Query: 89 LARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNSFHGRTLFT 148 +A+ + D +F +VF NSGAEANEAA KLAR Y N + ++Y+II NSFHGRT T Sbjct: 76 VAQIISDLSFGCKVFFCNSGAEANEAALKLARIYGNKKHNGKRYKIITMVNSFHGRTFAT 135 Query: 149 VNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKTCAVVLEPIQGEGGVLPAQQAY 208 + GQ K GF P + I H+P+ND++A + AI +T AVV+E IQGEGGV+PA++ Y Sbjct: 136 LAATGQEKVKKGFEPTLDFIKHIPFNDIDAFEKAIEPETVAVVMEVIQGEGGVIPAKEGY 195 Query: 209 LEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKSLGGGFPIGAMLT 268 L+ R++C E + LL+FDEVQ+G+GR GE+F Y Y V PDI + AK+LG GFPIGAM+ Sbjct: 196 LDAVRRICFEKDILLIFDEVQTGIGRTGEVFGYQLYDVKPDIFTLAKALGNGFPIGAMVA 255 Query: 269 TGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKHERFKSRLQKIGQE 328 EIA++LS GTH +T+GGN L A+A+ L+ ++ LD VK K K++L+ I Sbjct: 256 KTEIAEYLSPGTHASTFGGNYLGCAIAKYVLETVSDRSFLDSVKEKGNYLKNKLKTI--- 312 Query: 329 YGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASPDVVRFAPSLVIDDAE 388 +G EIRG G++IG L D D ++ A K V+ + A + VR P+L I Sbjct: 313 FGDMGEIRGEGMMIGVRLIDSI--SLSDFIDRAHKNGVLTVPAGDNTVRIYPALNISYDV 370 Query: 389 IDEGLERFERAVAK 402 ++EGLE + + + Sbjct: 371 LNEGLELINKTIGE 384 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: 389 Number of extensions: 14 Number of successful extensions: 3 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: 386 Length adjustment: 31 Effective length of query: 375 Effective length of database: 355 Effective search space: 133125 Effective search space used: 133125 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 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