Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate RR42_RS16955 RR42_RS16955 acetylornithine aminotransferase
Query= BRENDA::A0A140N9B6 (406 letters) >FitnessBrowser__Cup4G11:RR42_RS16955 Length = 395 Score = 292 bits (748), Expect = 1e-83 Identities = 160/362 (44%), Positives = 223/362 (61%), Gaps = 9/362 (2%) Query: 28 GEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNEPVLRLA 87 G+GS L D GK Y+DF G AVN LGH++ + +AL +Q+ K ++ + NEP+LRLA Sbjct: 25 GKGSWLTDHNGKRYLDFVQGWAVNCLGHSNQAMIDALVDQSKKLFNPSPAFYNEPMLRLA 84 Query: 88 KKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSG---IVAFKNAFHGRTLF 144 ++L DA+ D+VFF NSGAEANE A+KLARK+ HK+G I+ ++FHGRTL Sbjct: 85 RQLTDASCFDKVFFANSGAEANEGAIKLARKWGR----KHKNGAFEIITMDHSFHGRTLA 140 Query: 145 TVSAGGQPAYSQDFAPLPADIRHAAYNDINSASALIDDSTCAVIVEPIQGEGGVVPASNA 204 T+SA G+ + FAP A ND+ S LI+D T A+++EP+QGEGGV+PAS Sbjct: 141 TMSASGKAGWDTIFAPQVPGFPKADLNDLASVEKLINDKTVAIMLEPVQGEGGVIPASRE 200 Query: 205 FLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLTTAKALGGGFPVGALL 264 F+QGLR+L ++H L I DEVQTG GR G ++AY GV PD++T K +GGG P+ ALL Sbjct: 201 FMQGLRKLADQHKLLFIVDEVQTGCGRCGTMFAYELSGVEPDIMTLGKGIGGGVPLAALL 260 Query: 265 ATEECARVMTVGTHGTTYGGNPLASAVAGKVLELINTPEMLNGVKQRHDWFVERLNTINH 324 E A G G TY GNP+ +AV V+ + P L V+ + + E+L + Sbjct: 261 CKAEVAS-FEAGDQGGTYNGNPVMTAVGSAVISQLTAPGFLQSVQDKGAYLREQLLALTS 319 Query: 325 RYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVMVLIAGGNVVRFAPALNVSEE 384 +GL E RG GLL VLN D Q + +++ G+++ N++RF PALNV+ E Sbjct: 320 EFGLGGE-RGEGLLRALVLNKDIGPQLVEEARDMQPQGLLLNSPRPNLLRFMPALNVTIE 378 Query: 385 EV 386 E+ Sbjct: 379 EI 380 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: 423 Number of extensions: 23 Number of successful extensions: 4 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: 395 Length adjustment: 31 Effective length of query: 375 Effective length of database: 364 Effective search space: 136500 Effective search space used: 136500 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 Sep 17 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