Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_007473232.1 CMTB2_RS01220 glutamate-1-semialdehyde-2,1-aminomutase
Query= BRENDA::A0A3B6KM96 (472 letters) >NCBI__GCF_000170735.1:WP_007473232.1 Length = 420 Score = 125 bits (313), Expect = 4e-33 Identities = 95/327 (29%), Positives = 163/327 (49%), Gaps = 29/327 (8%) Query: 58 PMVFSKGEGSHILDPEGNKYIDFLSAYSAVNQGHCHPKVLRALIEQAERLTLSSRAFYND 117 P KGEG++I D EGNKY+D++ ++ + GHC A+IE A + +S A Sbjct: 29 PPFIEKGEGAYIFDIEGNKYLDYIQSWGPLIFGHCDKDTQNAIIE-AVKKGVSFGAPTKV 87 Query: 118 KFPVFAQYLTSMFGYDMMLPMNTGAEGVETAIKLARKWGYEKKNIPKNEALIVSCCGCFH 177 + + + L +++ +N+G E +AI+LAR GY K+ I+ GC+H Sbjct: 88 EVELAKEVLELFPHLNLIRFVNSGTEATMSAIRLAR--GYTGKDD------IIKFEGCYH 139 Query: 178 GRTLGVISMSCDNDATRGF--GPLVPGH-----LKVDFGDIDGLEKIFKEHGDRICGFLF 230 G + ++ + AT G P VP L + DI+ ++K F E+GD C + Sbjct: 140 GHSDSLLVSAGSGAATFGVPSSPGVPADFTKHTLLAKYNDIESVKKCF-ENGDVGC-VII 197 Query: 231 EPIQGEAGVIIPPDGYLKAVRDLCSRHNILMIDDEIQTGIARTGKMLACDWEGVRPDMVI 290 EPI G ++ +L +R++C+ + ++I DE+ +G R + D G++ D+V Sbjct: 198 EPIAGNMSLVPGEKEFLGELREICNHYGAVLIFDEVMSGF-RASLRGSFDIYGIKADIVT 256 Query: 291 LGKALGAGVVPVSAVLADKDIM---LCIKPGEHGSTFGGNPLASAVAIASLKVVKDEGLV 347 GK +G G +PV A K+IM + P T GNP+A + + +K +K+ Sbjct: 257 FGKVIGGG-MPVGAFAGKKEIMEKLSPVGPVYQAGTLSGNPVAMSAGLTVIKKLKEN--- 312 Query: 348 ERAAELGQEFRDQLRKVQQKFPDIIRE 374 E+ +E D+ +K+ + F +I +E Sbjct: 313 ---PEIYKELEDKAKKLMEGFSEISKE 336 Lambda K H 0.321 0.138 0.410 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: 455 Number of extensions: 27 Number of successful extensions: 5 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: 472 Length of database: 420 Length adjustment: 32 Effective length of query: 440 Effective length of database: 388 Effective search space: 170720 Effective search space used: 170720 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 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