Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_013092327.1 BC1002_RS22675 aspartate aminotransferase family protein
Query= BRENDA::A0A140N9B6 (406 letters) >NCBI__GCF_000092885.1:WP_013092327.1 Length = 442 Score = 150 bits (379), Expect = 7e-41 Identities = 122/410 (29%), Positives = 197/410 (48%), Gaps = 46/410 (11%) Query: 18 YASAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKF-----W 72 + +AP + +G G+E +D G+ GH+ E+ A+ +Q S + Sbjct: 23 FKAAPRLLESAKGMYYRSTDGREILDGCAGLWCVNAGHSRDEIVAAITQQLSTLDFAPTF 82 Query: 73 HTGNGYTNEPVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIV 132 G+ E ++A+ + + DR+FF NSG+E+ + ALK+A + R ++ ++ Sbjct: 83 QMGHPLAFEAATKVAELMPEGL--DRIFFTNSGSESVDTALKIALAYHRARGEGQRTRLI 140 Query: 133 AFKNAFHGRTLFTVSAGGQPAYSQDF--APLPA--------DIRHAAYN----------- 171 + +HG +S GG + F A LPA ++ H A++ Sbjct: 141 GRERGYHGVGFGGISVGGIAPNRKTFSGALLPAVDHLPHTHNLEHNAFSKGQPAWGAHLA 200 Query: 172 -DINSASALIDDST-CAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGV 229 ++ AL D ST AVIVEP+ G GV+ +LQ LRE+C +H LLIFDEV TG Sbjct: 201 EELERIVALHDASTIAAVIVEPVAGSTGVLIPPQGYLQKLREICTKHGILLIFDEVITGF 260 Query: 230 GRTGELYAYMHYGVTPDLLTTAKAL-GGGFPVGALLATEECARVMTVGT---------HG 279 GR G+ A H+GVTPDL+T AKA+ P+GA+ A+ + VG+ HG Sbjct: 261 GRLGKATASEHFGVTPDLITMAKAINNASIPMGAVAASRTIHDTV-VGSGAPGAIELFHG 319 Query: 280 TTYGGNPLASAVAGKVLELINTPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLI 339 TY +P A+A A L L ++ F + + + +VR LGL+ Sbjct: 320 YTYSAHPAAAAAAIATLNLYRRDQLFERAASLAPTFEAAAHGLRGAKHV-KDVRNLGLVA 378 Query: 340 GCVLNA-DYA--GQAKQISQEAAKAGVMVLIAGGNVVRFAPALNVSEEEV 386 G L + D A +A + + +AGV++ G+++ F+P L + EE++ Sbjct: 379 GIELESRDGAPGARAYEAFVKCFEAGVLIRFT-GDILAFSPPLIIDEEQI 427 Lambda K H 0.319 0.135 0.406 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: 422 Number of extensions: 26 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: 442 Length adjustment: 32 Effective length of query: 374 Effective length of database: 410 Effective search space: 153340 Effective search space used: 153340 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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