Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_109969430.1 DK846_RS13185 aspartate aminotransferase family protein
Query= BRENDA::P04181 (439 letters) >NCBI__GCF_003173355.1:WP_109969430.1 Length = 400 Score = 242 bits (617), Expect = 2e-68 Identities = 145/392 (36%), Positives = 218/392 (55%), Gaps = 31/392 (7%) Query: 60 VALERGKGIYLWDVEGRKYFDFLSSYSAVNQGHCHPKIVNALKSQVDKLTLTSRAFYNNV 119 +++E+G G+Y+WD G++Y DF S + GH +P I AL +Q K+ N Sbjct: 24 LSIEKGDGVYVWDENGKQYLDFTSGWGVTCIGHANPIITEALCNQSKKIIQNP-----NS 78 Query: 120 LGEYEEYITKLFN-YHKVLPM--------NTGVEAGETACKLARKWGYTVKGIQKYKAKI 170 Y ++L +H++LP N+G EA + A KLARK V G K I Sbjct: 79 GATYSPARSRLIQLFHEILPKHLTRIFFANSGAEANDAAIKLARK----VTG----KKNI 130 Query: 171 VFAAGNFWGRTLSAISSSTDPTSYDGFGPFMPGFDIIPYNDLPALERALQDPNVAAFMVE 230 + +F GRT+S +S++ + F P MPG+ +P+ND+ A++ + D +VAA +VE Sbjct: 131 ISTEMSFHGRTISTVSATGQDVHRNKFNPLMPGYFFVPFNDISAVKEII-DQDVAAVIVE 189 Query: 231 PIQGEAGVVVPDPGYLMGVRELCTRHQVLFIADEIQTGLARTGRWLAVDYENVRPDIVLL 290 PIQGE GV +P YL+ + E+C H VLFIADEIQTG RTG + +PDI+ + Sbjct: 190 PIQGEGGVNIPSESYLLELSEVCREHGVLFIADEIQTGFFRTGPLFYSISKGAKPDIITM 249 Query: 291 GKALSGGLYPVSAVLCDDDIMLTIKPGEHGSTYGGNPLGCRVAIAALEVLEEENLAENAD 350 K ++GG +P SA D+++ I+ G+HG TY GNPLGC V+ A + L + ++ + Sbjct: 250 AKGIAGG-FPFSAFAVTDEVVNGIQKGDHGGTYNGNPLGCAVSEAVIRYLIDSDIESHVS 308 Query: 351 KLGIILRNEL----MKLPSDVVTAVRGKGLLNAIVIKETKDWDAWKVCLRLRDNGLLAKP 406 LGI L K P +T VRG+GLL I ++ T D + ++ R DNGL+ Sbjct: 309 DLGIDTIKRLNGWKEKYPK-AITEVRGQGLL--IALELTDDLKSAEIVTRCLDNGLILNL 365 Query: 407 THGDIIRFAPPLVIKEDELRESIEIINKTILS 438 HG IIR P L I + E++ ++I+ K I++ Sbjct: 366 KHGHIIRIFPALTITKQEMQTGLDILEKEIVT 397 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: 424 Number of extensions: 22 Number of successful extensions: 7 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: 400 Length adjustment: 32 Effective length of query: 407 Effective length of database: 368 Effective search space: 149776 Effective search space used: 149776 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 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