Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_044410795.1 NA59_RS08125 aspartate aminotransferase family protein
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >NCBI__GCF_000934765.1:WP_044410795.1 Length = 392 Score = 279 bits (714), Expect = 9e-80 Identities = 160/375 (42%), Positives = 222/375 (59%), Gaps = 9/375 (2%) Query: 14 MMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWH 73 +M YA V GEG+ L+D+QG+ Y+D GIAV +LGHAHP + AL EQ+ K H Sbjct: 5 LMNTYARLPITFVEGEGATLYDEQGRAYLDAVSGIAVCSLGHAHPEIAHALCEQSKKLIH 64 Query: 74 TGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVA 133 T N Y LA +LI + D+VFF NSGAEANE A+K+ARKY +D+ G I+ Sbjct: 65 TSNLYHVVNQQLLADELIRLSGMDKVFFGNSGAEANEGAIKIARKYGNDQ-GKTNPEILV 123 Query: 134 FKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALIDD--NTCAVIVEP 191 +N+FHGRT+ T+SA G + F PL ++D+ + + I N A++VEP Sbjct: 124 MENSFHGRTMATLSATGSQKVQEGFHPLVSGFVRVPFDDIAAVEQKIASHPNLVAILVEP 183 Query: 192 MQGEGGV-VPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLST 250 +QGEGGV VP D +L+ LR LCD HN LL+ DE+QTGVGRTG+ +A+ H + PD+LS Sbjct: 184 VQGEGGVHVPKDG-YLKALRALCDQHNLLLMIDEIQTGVGRTGKWFAFQHEDILPDVLSL 242 Query: 251 AKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLNGVKQ 310 AKALG G PIGA LA + A V+ G HGTT+GGNPLACA V TI ++ V + Sbjct: 243 AKALGNGVPIGACLARGKAAEVLAPGNHGTTFGGNPLACAAGLAVIKTIEHHNFIDYVAK 302 Query: 311 RHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEEGLMILIAGA 370 + + A A K++RG G +IG L D G+ + +A ++ L+I + Sbjct: 303 QGEIMISDFKARLAGIEQVKQVRGKGYMIGIQL-DRPCGE---LVKRALDKNLLINVTRG 358 Query: 371 NVVRFAPALIISEDE 385 + +R P ++S + Sbjct: 359 DTIRLLPPFVMSHTQ 373 Lambda K H 0.321 0.137 0.412 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: 439 Number of extensions: 16 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: 392 Length adjustment: 31 Effective length of query: 375 Effective length of database: 361 Effective search space: 135375 Effective search space used: 135375 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: 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