Align lysine decarboxylase (EC 4.1.1.18) (characterized)
to candidate BWI76_RS07195 BWI76_RS07195 lysine decarboxylase CadA
Query= BRENDA::A0A094XEM2 (715 letters) >FitnessBrowser__Koxy:BWI76_RS07195 Length = 715 Score = 1446 bits (3742), Expect = 0.0 Identities = 702/715 (98%), Positives = 715/715 (100%) Query: 1 MNVIAIMNHMGVYFKEEPIRELHRALERLDFRIVYPNDRDDLLKLIENNSRLCGVIFDWD 60 MNVIAIMNHMGVYFKEEPIRELHRALERLDFRIVYPNDRDDLLKLIENN+RLCGVIFDWD Sbjct: 1 MNVIAIMNHMGVYFKEEPIRELHRALERLDFRIVYPNDRDDLLKLIENNARLCGVIFDWD 60 Query: 61 KYNLELCEEISKMNEYMPLYAFANTYSTLDVSLNDLRMQVRFFEYALGAAEDIANKIKQN 120 KYNLELCE+ISKMNEYMPLYAFANTYSTLDVSLNDLRMQVRFFEYALGAAEDIANKIKQN Sbjct: 61 KYNLELCEDISKMNEYMPLYAFANTYSTLDVSLNDLRMQVRFFEYALGAAEDIANKIKQN 120 Query: 121 TDEYIDTILPPLTKALFKYVREGKYTFCTPGHMGGTAFQKSPVGSIFYDFFGSNTMKSDI 180 TDEYIDTILPPLTKALFKYVREGKYTFCTPGHMGGTAFQKSPVGSIFYDFFGSNTMKSDI Sbjct: 121 TDEYIDTILPPLTKALFKYVREGKYTFCTPGHMGGTAFQKSPVGSIFYDFFGSNTMKSDI 180 Query: 181 SISVSELGSLLDHSGPHKEAEEYIARVFNAERSYMVTNGTSTANKIVGMYSAPAGSTVLI 240 SISVSELGSLLDHSGPHKEAEEYIARVFNAERSYMVTNGTSTANKIVGMYSAPAGSTVLI Sbjct: 181 SISVSELGSLLDHSGPHKEAEEYIARVFNAERSYMVTNGTSTANKIVGMYSAPAGSTVLI 240 Query: 241 DRNCHKSLTHLMMMSDITPIYFRPTRNAYGILGGIPQSEFQHATIAKRVKETPNATWPVH 300 DRNCHKSLTHLMMMSDITPIYFRPTRNAYGILGGIPQSEFQHATIAKRVKETPNATWPVH Sbjct: 241 DRNCHKSLTHLMMMSDITPIYFRPTRNAYGILGGIPQSEFQHATIAKRVKETPNATWPVH 300 Query: 301 AVITNSTYDGLLYNTDFIKKTLDVKSIHFDSAWVPYTNFSPIYEGKCGMSGGRVEGKVIY 360 AVITNSTYDGLLYNTD+IKKTLDVKSIHFDSAWVPYTNFSPIYEGKCGMSGGRVEGKVIY Sbjct: 301 AVITNSTYDGLLYNTDYIKKTLDVKSIHFDSAWVPYTNFSPIYEGKCGMSGGRVEGKVIY 360 Query: 361 ETQSTHKLLAAFSQASMIHVKGDVNEETFNEAYMMHTTTSPHYGIVASTETAAAMMRGNA 420 ETQSTHKLLAAFSQASMIHVKGDVNEETFNEAYMMHTTTSPHYG+VASTETAAAMM+GNA Sbjct: 361 ETQSTHKLLAAFSQASMIHVKGDVNEETFNEAYMMHTTTSPHYGVVASTETAAAMMKGNA 420 Query: 421 GKRLIDGSIERSIKFRKEIKRLKGESEGWFFDVWQPEHIDGAECWPLRSDSAWHGFKNID 480 GKRLIDGSIERSIKFRKEIKRLKGES+GWFFDVWQPEHIDGAECWPLRSDSAWHGFKNID Sbjct: 421 GKRLIDGSIERSIKFRKEIKRLKGESDGWFFDVWQPEHIDGAECWPLRSDSAWHGFKNID 480 Query: 481 NEHMYLDPIKVTLLTPGMKKDGTMDDFGIPASIVAKYLDEHGIVVEKTGPYNLLFLFSIG 540 NEHMYLDPIKVTLLTPGMKKDGTMDDFGIPASIVAKYLDEHGIVVEKTGPYNLLFLFSIG Sbjct: 481 NEHMYLDPIKVTLLTPGMKKDGTMDDFGIPASIVAKYLDEHGIVVEKTGPYNLLFLFSIG 540 Query: 541 IDKTKALSLLRALTDFKRAFDLNLRVKNMLPSLYREDPEFYENMRIQDLAQNIHKLVEHH 600 IDKTKALSLLRALTDFKRAFDLNLRVKNMLPSLYREDPEFYENMR+Q+LAQNIHKL+EHH Sbjct: 541 IDKTKALSLLRALTDFKRAFDLNLRVKNMLPSLYREDPEFYENMRVQELAQNIHKLIEHH 600 Query: 601 NLPDLMFRAFEVLPSMVMTPYAAFQKELHGQTEEVYLEEMVGRVNANMILPYPPGVPLVM 660 NLPDLMFRAFEVLP+M++TPYAAFQKELHGQTEEVYLEEMVGRVNANMILPYPPGVPLVM Sbjct: 601 NLPDLMFRAFEVLPTMMITPYAAFQKELHGQTEEVYLEEMVGRVNANMILPYPPGVPLVM 660 Query: 661 PGEMITEESRPVLEFLQMLCEIGAHYPGFETDIHGAYRQADGRYTVKVLKEENNK 715 PGEMITEESRPVLEFLQMLCEIGAHYPGFETDIHGAYRQADGRYTVKVL+EENNK Sbjct: 661 PGEMITEESRPVLEFLQMLCEIGAHYPGFETDIHGAYRQADGRYTVKVLREENNK 715 Lambda K H 0.320 0.136 0.408 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: 1826 Number of extensions: 35 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: 715 Length of database: 715 Length adjustment: 39 Effective length of query: 676 Effective length of database: 676 Effective search space: 456976 Effective search space used: 456976 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: 55 (25.8 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