Align lysine 6-dehydrogenase (EC 1.4.1.18) (characterized)
to candidate Ac3H11_2284 putative dehydrogenase
Query= BRENDA::Q3S559 (368 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2284 Length = 369 Score = 484 bits (1246), Expect = e-141 Identities = 252/362 (69%), Positives = 284/362 (78%) Query: 4 TQHAITVLGAGKIGFAIALLLQRTGDYAVCVADQDPSRLDAVAALGCQTAQIDNDAALEA 63 T+H +T+LGAG IGFA+ALLLQ+ GDY + +AD+DP+RL VAALG T + +D +L++ Sbjct: 7 TRHTVTILGAGHIGFAMALLLQQAGDYDILMADRDPARLAEVAALGVATRLVGDDTSLQS 66 Query: 64 AIAGRHAVLNALPFHRAVAVAGLCARLGVHYFDLTEDVASTHAIHALGRDARAVLMPQCG 123 AIAGR AVLNALPFHRAV VA LCA GVHYFDLTEDVAST AI AL AR+VLMPQCG Sbjct: 67 AIAGRFAVLNALPFHRAVPVATLCAAAGVHYFDLTEDVASTQAIRALAAKARSVLMPQCG 126 Query: 124 LAPGFIGIVGNDLARRFDTLLDLRMRVGGLPRYPTNALRYNLYLEHRGADQRVLQSMRGA 183 LAPGFIGIVGNDLARRFDTL LRMRVG LPRYP ALRYNL G Sbjct: 127 LAPGFIGIVGNDLARRFDTLHTLRMRVGALPRYPQGALRYNLTWSTEGLINEYCNPCEAI 186 Query: 184 VDGELVKVPPMEGYETFTLDGVEYEAFNTSGGLGTLPQTLLGKARNVDYKSVRYPGHCAI 243 VDG VP +EG ETF LDGVEYEAFNTSGGLGTL +TL GKAR VDY+S+RYPGH AI Sbjct: 187 VDGVRTTVPALEGLETFALDGVEYEAFNTSGGLGTLTETLAGKARQVDYQSIRYPGHNAI 246 Query: 244 MKLLLNDLRLRERRELLQDILESAIPATGQDVIVILATASGYRGGRLLQEAYSAHIHGDT 303 +KLLLNDLRLR+RR+LL+DILESAIP T QDVIVI ATA+G RGGRL+QE+YSA I G Sbjct: 247 LKLLLNDLRLRDRRDLLKDILESAIPTTDQDVIVIFATAAGLRGGRLVQESYSARIVGTE 306 Query: 304 VDGHALSAIQLSTAAGICTALDLVVEGALPQRGFVGQESIPLDALLANRHGRIYAGQRLD 363 + GH LSAIQL+TAAGICTALDLV +G LPQRGFVGQE++ L LANR G YAG+ Sbjct: 307 LAGHRLSAIQLTTAAGICTALDLVAQGRLPQRGFVGQEAVRLGDFLANRFGVAYAGEGAL 366 Query: 364 AL 365 AL Sbjct: 367 AL 368 Lambda K H 0.323 0.139 0.405 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: 441 Number of extensions: 15 Number of successful extensions: 1 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: 368 Length of database: 369 Length adjustment: 30 Effective length of query: 338 Effective length of database: 339 Effective search space: 114582 Effective search space used: 114582 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 (21.9 bits) S2: 49 (23.5 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