Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_011383255.1 AMB_RS04150 acetylornithine transaminase
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >NCBI__GCF_000009985.1:WP_011383255.1 Length = 388 Score = 332 bits (851), Expect = 1e-95 Identities = 180/393 (45%), Positives = 243/393 (61%), Gaps = 11/393 (2%) Query: 10 FDEWMMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAG 69 F + ++PV+ I +GEG+ L G+ ++DF G+AVNALGHAHPRLV AL QAG Sbjct: 2 FPDNLLPVFDRTDVIFEQGEGAWLTASDGRRFLDFGAGVAVNALGHAHPRLVAALEAQAG 61 Query: 70 KFWHTGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKS 129 K WH N Y R+A++LI A+FAD FFCN+GAEA E +K+AR+Y H E++ Sbjct: 62 KLWHCSNLYRVPGQERVAERLIKASFADTAFFCNTGAEAMELVIKIARRYHHCAGRPERN 121 Query: 130 GIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALIDDNTCAVIV 189 IVA +FHGRT+ T++A G P Y + F P+ H Y DL++A+ I NT A++V Sbjct: 122 RIVACTGSFHGRTIATLAAAGTPKYLEGFGPVAQGFDHVPYGDLEAARGAIGSNTAALLV 181 Query: 190 EPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLS 249 EP+QGEGG+ PAD +LRGLR L D LL+ DEVQTG+GRTG+L+A+ G+ PD++ Sbjct: 182 EPVQGEGGIRPADPAYLRGLRALADQFGLLLLMDEVQTGIGRTGKLFAHEWSGIAPDVMG 241 Query: 250 TAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLNGVK 309 AK LGGGFP+GA+LA+E+ AS MT GTHG T+GGNPLA AVA V + L V+ Sbjct: 242 LAKGLGGGFPVGAVLATEKAASCMTPGTHGCTFGGNPLAMAVAEAVLDEVMAPGFLERVQ 301 Query: 310 QRHQWFCERLNAINARY-GLFKEIRGLGLLIG---CVLKDEYAGKAKAISNQAAEEGLMI 365 RL+ + RY G ++RG GL++G + E+ K A GL+ Sbjct: 302 AVAALLRGRLDDLARRYPGAIAQVRGQGLMLGLKTVPVNTEFNAKLFA-------AGLLA 354 Query: 366 LIAGANVVRFAPALIISEDEVNSGLDRFELACK 398 + AG NVVR P LII E EV ++ + C+ Sbjct: 355 VGAGDNVVRLVPPLIIGEAEVERAVEIIDGVCR 387 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: 453 Number of extensions: 23 Number of successful extensions: 2 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: 388 Length adjustment: 31 Effective length of query: 375 Effective length of database: 357 Effective search space: 133875 Effective search space used: 133875 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