Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate CCNA_00620 CCNA_00620 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase
Query= BRENDA::P9WQ77 (449 letters) >FitnessBrowser__Caulo:CCNA_00620 Length = 392 Score = 147 bits (370), Expect = 8e-40 Identities = 126/414 (30%), Positives = 176/414 (42%), Gaps = 49/414 (11%) Query: 37 LDLTRSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNS 96 +D+ R G +L D GR YLD+ VA + LG P LV + A+++ A N Sbjct: 13 IDIVRGEGCWLYDQ-DGRDYLDLAAGVAVNTLGHGDPRLVQALKTQADILWHASNLYRLP 71 Query: 97 DVYSVAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPAL 156 ++A TFA +FF GA AVE A+K A W+ + Sbjct: 72 AQEALATKLTDATFA--------DRVFFANSGAEAVEAAIKTARRWQGAKGRPERY---- 119 Query: 157 GTQVLHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAE 216 +VL AFHGR+ T+S T+ P +D A + Sbjct: 120 --RVLTFGNAFHGRTLATISATDQMKVREGFTPLYD-------------------AFDTT 158 Query: 217 ALRQARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTG 276 A A + EPIQGEGG P F A +R LCD+ D LLI DEVQTG Sbjct: 159 PFNDIEGAARAITPQTAAILVEPIQGEGGLTPATPGFLAGLRALCDQHDLLLILDEVQTG 218 Query: 277 CGLTGTAWAYQQLDVAPDIVAFGKKTQVCGVMAGRRV------DEVADNVFAVPSRLNST 330 G TG +A++ V PDI+A K G+ G + ++ A + P ST Sbjct: 219 IGRTGHLFAHELYGVRPDIIAVAK-----GLGGGFPIGACLATEDAASGM--TPGSHGST 271 Query: 331 WGGNLTDMVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCA 390 +GGN A +L+ + A G E + + A L+ L + + +G GLM Sbjct: 272 YGGNPLACAVASAVLDAVLAPGFLETVRERAALVDALLERLLRRHSDLFVRAQGHGLM-- 329 Query: 391 FSLPTTADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSA 444 L A +++ L V+ + AGAD VR PPLT+S EI A A + A Sbjct: 330 RGLQVRASARDVVAHLRDFGVMTVAAGADVVRLLPPLTISELEIAEAEARLLRA 383 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: 426 Number of extensions: 24 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: 392 Length adjustment: 32 Effective length of query: 417 Effective length of database: 360 Effective search space: 150120 Effective search space used: 150120 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