Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_092344171.1 BLU87_RS01565 aspartate aminotransferase family protein
Query= BRENDA::A0A140N9B6 (406 letters) >NCBI__GCF_900107645.1:WP_092344171.1 Length = 460 Score = 179 bits (453), Expect = 2e-49 Identities = 126/408 (30%), Positives = 207/408 (50%), Gaps = 43/408 (10%) Query: 22 PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGN--GYT 79 P +G+G+ + D G YID G V ALGH+HP++ +A +E HT + Sbjct: 49 PMAMAKGKGATIEDVDGNIYIDMFSGAGVMALGHSHPDVLKASHEAIEDITHTLDIPSPI 108 Query: 80 NEPVLRLAKKLIDATFADRVFFCN-SGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAF 138 + +++ KK++ RVFF +G++A E A+KLA KF RYG ++AF+ ++ Sbjct: 109 RQRMVKSMKKILPKELT-RVFFGGPTGSDAVEQAIKLA-KFNTGRYG-----VIAFEGSY 161 Query: 139 HGRTLFTVSAGGQPAYSQDFAPLPADIRHAAY------------NDINSASA-----LID 181 HG T ++ + Q PL ++ Y D+ +A ++ Sbjct: 162 HGMTGMALALTCDAHHRQGLGPLSPGVQFLPYPYEYRNPFGCPDEDLQLQAAENLERVLS 221 Query: 182 DS------TCAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGEL 235 DS AVI+E +QGEGG + + FLQ +RE+C +H+ ++I DE+Q G+GRTG++ Sbjct: 222 DSHSGYLKPAAVILESVQGEGGTIIPAPIFLQRVREICTKHDIVMICDEIQAGLGRTGKM 281 Query: 236 YAYMHYGVTPDLLTTAKALGG-GFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGK 294 +A+ H G+ PD++T +KALGG GFP+ A+ EE T T G T+ GN +A A Sbjct: 282 FAFEHAGIVPDIVTMSKALGGIGFPISAIAYREELNTWPTGLTIG-TFRGNMIAFAAGSA 340 Query: 295 VLELINTPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQ---- 350 LE + ++ + + +L + + + E RGLG+++ + D + Sbjct: 341 ALEWMQDNGVIEHAAGLGEKCMVKLKELEAQSAIVGESRGLGMMLAIEMVKDKESREPAG 400 Query: 351 --AKQISQEAAKAGVMVLIAG--GNVVRFAPALNVSEEEVTTGLDRFA 394 AK + + A GVM+ + G GNV R P L ++E+ G++ A Sbjct: 401 DYAKLVRKHAHLRGVMIEVGGHHGNVARLLPPLIITEDLAMKGIEIIA 448 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: 440 Number of extensions: 19 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: 460 Length adjustment: 32 Effective length of query: 374 Effective length of database: 428 Effective search space: 160072 Effective search space used: 160072 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