Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_073038500.1 BUB04_RS08170 putrescine aminotransferase
Query= BRENDA::B1A0U3 (469 letters) >NCBI__GCF_900129305.1:WP_073038500.1 Length = 449 Score = 224 bits (571), Expect = 5e-63 Identities = 140/388 (36%), Positives = 213/388 (54%), Gaps = 21/388 (5%) Query: 59 KGSSVWDPEGNKYIDFLSGYSAVNQGHCHPKILKALHDQADRLTVSSRAFYNDRFPVFAE 118 +GS + D G +YID L G+ + G HPK++ A+ Q DR S+ + + Sbjct: 71 QGSILRDALGREYIDALGGFGLYSLGIRHPKVVAAVKAQLDRSPQYSQEMLDPLRAHLGK 130 Query: 119 YLTALFGYDMVLPM--NTGAEGVETALKLARKWGYEKKKIPNDEALIVSCCGCFNGRTLG 176 + A+ D+ N+G E VE A+KLA K + ++ F+G+TLG Sbjct: 131 VIAAITPGDIQYGFFANSGTEAVEGAMKLA--------KFYTGKPGFIAMLRGFHGKTLG 182 Query: 177 VISMSCDNEATRGFGPLMPGHLKVDFGDAEAIERIF---KEKGDRVAAFILEPIQGEAGV 233 +S+ + + PL+ G V FGDA+A+E+ K GD +AA + EPIQGEAG Sbjct: 183 SLSLMGKSVFRQPLLPLLEGVRHVPFGDADAVEKALAAAKAVGDGIAAVVAEPIQGEAGA 242 Query: 234 VIPPDGYLKAVRDLCSKYNVLMIADEIQTGLARTGKMLACDWEDVRPDVVILGKALGGGI 293 ++PPD + +R+LC Y VL+IADE+QTG RTG + D DV PD++ GKALGGG+ Sbjct: 243 IVPPDDFWPRLRELCDHYGVLLIADEVQTGFGRTGTLFGVDHWDVTPDIMCFGKALGGGV 302 Query: 294 LPVSAVLADKDVMLCIKPG--QHGSTFGGNPLASAVAIAALEVIKEERLTERSTKLGGEL 351 +P+SA + + ++P H +T GGNPLA A A+A + V E L ++ + G + Sbjct: 303 VPMSAFFSTPKIWKVMEPNPFMHTTTTGGNPLACAAALAQITVTLGEDLPRQAAEKGDYV 362 Query: 352 LGLLHKIQKKHPEHVKEVRGKGLFIGVELNSESLSPVSGFELSEKLKERGVLAKS--THD 409 LG L + Q + P+ ++EVRGKGL IG+E ++ + GF+++ L RGVL T+ Sbjct: 363 LGKLREFQSRFPQILQEVRGKGLLIGMEFPTDEV----GFKVAAGLFSRGVLTAGTLTNA 418 Query: 410 TIIRFTPPLCISADEIQQGSKALAEVLE 437 IR P L IS + + + L + L+ Sbjct: 419 QTIRIEPALNISYELLDELLNRLEDTLK 446 Lambda K H 0.319 0.137 0.409 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: 456 Number of extensions: 20 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: 469 Length of database: 449 Length adjustment: 33 Effective length of query: 436 Effective length of database: 416 Effective search space: 181376 Effective search space used: 181376 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