Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate WP_011383255.1 AMB_RS04150 acetylornithine transaminase
Query= BRENDA::P9WQ77 (449 letters) >NCBI__GCF_000009985.1:WP_011383255.1 Length = 388 Score = 142 bits (358), Expect = 2e-38 Identities = 128/415 (30%), Positives = 184/415 (44%), Gaps = 47/415 (11%) Query: 31 DGLDIVLDLTRSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAAL 90 D D++ + + G++L A GRR+LD VA +ALG P LV E A + Sbjct: 11 DRTDVIFE--QGEGAWLT-ASDGRRFLDFGAGVAVNALGHAHPRLVAALEAQAGKLWHCS 67 Query: 91 NKPSNSDVYSVAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAH 150 N VA +FA D A FF GA A+E +K A R++ Sbjct: 68 NLYRVPGQERVAERLIKASFA----DTA----FFCNTGAEAMELVIKIA----RRYHHCA 115 Query: 151 GIDPALGTQVLHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAM 210 G +++ G+FHGR+ TL+ T + P + G D Sbjct: 116 GRPER--NRIVACTGSFHGRTIATLAAAGTPKYLEGFGP-----------VAQGFDHVPY 162 Query: 211 AALEAEALRQARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIF 270 LEA AR A + + A + EP+QGEGG R P + +R L D+F LL+ Sbjct: 163 GDLEA-----ARGAIGS---NTAALLVEPVQGEGGIRPADPAYLRGLRALADQFGLLLLM 214 Query: 271 DEVQTGCGLTGTAWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFA----VPSR 326 DEVQTG G TG +A++ +APD++ K G+ G V V A P Sbjct: 215 DEVQTGIGRTGKLFAHEWSGIAPDVMGLAK-----GLGGGFPVGAVLATEKAASCMTPGT 269 Query: 327 LNSTWGGNLTDMVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRG 386 T+GGN M A +L+ + A G ER LR RLD+LA +P + RG+G Sbjct: 270 HGCTFGGNPLAMAVAEAVLDEVMAPGFLERVQAVAALLRGRLDDLARRYPGAIAQVRGQG 329 Query: 387 LMCAFSLPTTADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAV 441 LM L T E +L+ ++ + AG + VR PPL + AE++ A+ + Sbjct: 330 LM--LGLKTVPVNTEFNAKLFAAGLLAVGAGDNVVRLVPPLIIGEAEVERAVEII 382 Lambda K H 0.323 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: 420 Number of extensions: 14 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: 449 Length of database: 388 Length adjustment: 32 Effective length of query: 417 Effective length of database: 356 Effective search space: 148452 Effective search space used: 148452 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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