Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate SMc02138 SMc02138 acetylornithine transaminase
Query= BRENDA::P9WQ77 (449 letters) >FitnessBrowser__Smeli:SMc02138 Length = 399 Score = 142 bits (358), Expect = 2e-38 Identities = 128/415 (30%), Positives = 184/415 (44%), Gaps = 41/415 (9%) Query: 37 LDLTRSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNS 96 L R G +L+ A G RYLD VA ++LG P LV+ + A+ + N + Sbjct: 16 LRFERGEGVWLI-AEDGTRYLDFAAGVAVNSLGHAHPHLVEALKAQADKVWHLSNLYEIA 74 Query: 97 DVYSVAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPAL 156 S+A TFA +FF GA A+E A+K A R++ A G Sbjct: 75 GQESLARRLTQVTFA--------DRVFFTNSGAEALECAIKTA----RRYHFAKGHVEKF 122 Query: 157 GTQVLHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEA- 215 V+ GAFHGR+ T++ + I PK PG + + A Sbjct: 123 --HVITFEGAFHGRTLATIAAGGQQKYIEGFGPK-----------APGFYQVPFGDIGAV 169 Query: 216 -EALRQARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQ 274 A+ + AA + EPIQGEGG R EF +RELCDEF LLI DEVQ Sbjct: 170 KNAINEETAAI----------LVEPIQGEGGIRTASKEFMQGLRELCDEFGLLLILDEVQ 219 Query: 275 TGCGLTGTAWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFAVPSRLNSTWGGN 334 +G G TG +A++ + PDI+A K G G + A V ST+GGN Sbjct: 220 SGVGRTGKLFAHEWAGIKPDIMAVAKGIG-GGFPLGACLATEAAAAGMVAGTHGSTYGGN 278 Query: 335 LTDMVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFSLP 394 M +L+V+ AEG ++ + R L L FP V+ + RG GLM + Sbjct: 279 PLAMAVGNAVLDVVLAEGFLDQVREVALVFRQGLASLKDRFPDVIEEIRGDGLM--LGIK 336 Query: 395 TTADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSALPVVT 449 +L++ + ++V+PAG + +R PPL + AE +A + A V+ Sbjct: 337 AKVPSADLLKAIRAEKLLVVPAGENVLRLLPPLITTPAEAREGLARLERAAEAVS 391 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: 379 Number of extensions: 18 Number of successful extensions: 6 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: 399 Length adjustment: 32 Effective length of query: 417 Effective length of database: 367 Effective search space: 153039 Effective search space used: 153039 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