Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_028950476.1 Q385_RS0104250 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= BRENDA::P04181 (439 letters) >NCBI__GCF_000619805.1:WP_028950476.1 Length = 453 Score = 171 bits (434), Expect = 3e-47 Identities = 137/426 (32%), Positives = 206/426 (48%), Gaps = 55/426 (12%) Query: 60 VALERGKGIYLWDVEGRKYFDFLSSYSAVNQGHCHPKIVNALKSQVDKLTLTSRAFYNNV 119 V +ERG+G Y++D+ G KY D ++S GH HPK+ A+ QV K++ + +NV Sbjct: 30 VIVERGEGNYIYDIFGNKYLDGVASLWCNVHGHNHPKLNKAICDQVSKISHFTTLGASNV 89 Query: 120 LG-----EYEEYITKLFNYHKVLPMNTGVEAGETACKLARKWGYTVKGIQKYKAKIVFAA 174 + E K N KV G EA E A K+A + + KG K K K + + Sbjct: 90 PAIILAKKLVEITPKSLN--KVFYSEDGSEAMEIAIKIAYHYWHN-KGY-KEKTKFITLS 145 Query: 175 GNFWGRTLSAISSSTDPTSYDGFGPFMPGFDII----PYN---DLPALERALQ------- 220 + G T+ ++S ++ + P + FD+ PY ++ E+AL+ Sbjct: 146 QAYHGDTIGSVSVGGINIFHEKYKPLL--FDVYKLPSPYLKAVEIAGREKALEYETTKKL 203 Query: 221 -----------DPNVAAFMVEP-IQGEAGVVVPDPGYLMGVRELCTRHQVLFIADEIQTG 268 +A F++E +QG AG++ GYL V +C + VL I DE+ TG Sbjct: 204 IEEVEEFVFEHHQTIAGFVLEASVQGAAGILPFPKGYLKEVERICREYNVLMIVDEVATG 263 Query: 269 LARTGRWLAVDYENVRPDIVLLGKALSGGLYPVSAVLCDDDIMLTI-------KPGEHGS 321 RTG A ENV PDI+ LGK ++GG P++A L D+I K HG Sbjct: 264 FGRTGEMFACIKENVNPDIMALGKGITGGYLPLAATLTTDEIFEAFLGDFGEAKHFYHGH 323 Query: 322 TYGGNPLGCRVAIAALEVLEEENLAENADKLGIILRNELMK-LPSDVVTAVRGKGLLNAI 380 TY GNP+ C VA+A +++ EEE EN K IL L + L + V VR GL+ + Sbjct: 324 TYTGNPVACNVALANIDLFEEEKTLENVRKNIDILEKRLPEFLQLNHVIDVRNYGLMAGV 383 Query: 381 -VIKETK--------DWDAWKVCLRLRDNGLLAKPTHGDIIRFAPPLVIKEDELRESIEI 431 +IK+ K D +KV + G+ +P GD++ PPL IKEDEL + Sbjct: 384 ELIKDKKTKQPYPYGDRTGFKVAKAMLKRGIWVRPL-GDVMVIMPPLSIKEDELNYFLNS 442 Query: 432 INKTIL 437 + ++I+ Sbjct: 443 LKESII 448 Lambda K H 0.319 0.138 0.415 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: 489 Number of extensions: 26 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: 439 Length of database: 453 Length adjustment: 32 Effective length of query: 407 Effective length of database: 421 Effective search space: 171347 Effective search space used: 171347 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 Sep 24 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