Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate PP_4140 PP_4140 lysine decarboxylase
Query= SwissProt::Q9I2S7 (751 letters) >FitnessBrowser__Putida:PP_4140 Length = 749 Score = 1197 bits (3097), Expect = 0.0 Identities = 586/751 (78%), Positives = 657/751 (87%), Gaps = 4/751 (0%) Query: 1 MYKDLKFPVLIVHRDIKADTVAGERVRGIAHELEQDGFSILSTASSAEGRIVASTHHGLA 60 MYKDLKFP+LIVHR IKAD+VAGERVRGIA EL QDGF+IL+ A AE R+VA+THHGLA Sbjct: 1 MYKDLKFPILIVHRAIKADSVAGERVRGIAEELRQDGFAILAAADHAEARLVAATHHGLA 60 Query: 61 CILVAAEGAGENQRLLQDVVELIRVARVRAPQLPIFALGEQVTIENAPAESMADLHQLRG 120 C+L+AAEGAGEN LLQ++ ELIR+AR+RAP LPIFALGEQVT+ENAPAE+M++L+QLRG Sbjct: 61 CMLIAAEGAGENTHLLQNMAELIRLARLRAPNLPIFALGEQVTLENAPAEAMSELNQLRG 120 Query: 121 ILYLFEDTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYRKS 180 ILYLFEDTVPFLARQVARAA YL GLLPPFF+ALV+HTAQSNYSWHTPGHGGGVAY KS Sbjct: 121 ILYLFEDTVPFLARQVARAAHTYLDGLLPPFFKALVQHTAQSNYSWHTPGHGGGVAYHKS 180 Query: 181 PVGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVINGTS 240 PVGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAE RAARNFGADHTFFVINGTS Sbjct: 181 PVGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEARAARNFGADHTFFVINGTS 240 Query: 241 TANKIVWHSMVGREDLVLVDRNCHKSILHSIIMTGAIPLYLTPERNELGIIGPIPLSEFS 300 TANKIVWH+MVGR+DLVLVDRNCHKS++H+IIMTGAIPLYL PERNELGIIGPIPLSEFS Sbjct: 241 TANKIVWHAMVGRDDLVLVDRNCHKSVVHAIIMTGAIPLYLCPERNELGIIGPIPLSEFS 300 Query: 301 KQSIAAKIAASPLARGREPKVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFDEAWYA 360 ++IAAKI A+PLAR R ++KLAVVTNSTYDGLCY+A LIKQ LG SVEVLHFDEAW+A Sbjct: 301 PEAIAAKIQANPLARDRGQRIKLAVVTNSTYDGLCYHAGLIKQALGASVEVLHFDEAWFA 360 Query: 361 YAAFHEFYDGRYGMGTSRSEEGPLVFATHSTHKMLAAFSQASMIHVQDGGTRKLDVARFN 420 YAAFH+F+ GRY MGT+ + + PLVF+THSTHK+LAAFSQASMIHVQDG R+LD RFN Sbjct: 361 YAAFHDFFTGRYAMGTACAADSPLVFSTHSTHKLLAAFSQASMIHVQDGARRQLDRDRFN 420 Query: 421 EAFMMHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALANVRQNLDRND 480 EAFMMHISTSPQY I+ASLDVAS MMEGPAGRSL+QE FDEALSFRRALAN+R+++ D Sbjct: 421 EAFMMHISTSPQYSILASLDVASTMMEGPAGRSLLQEMFDEALSFRRALANLREHIAAAD 480 Query: 481 WWFGVWQPEQVEGTDQVGTHDWVLEPSADWHGFGDIAEDYVLLDPIKVTLTTPGLSAGGK 540 WWF +WQP EG ++ DW+L+P A WHGFG++ DYVLLDP+KVTL PGLSA G Sbjct: 481 WWFSIWQPPSAEGIPRLAAQDWLLQPGAQWHGFGEVVTDYVLLDPLKVTLVMPGLSADGV 540 Query: 541 LSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLVTELLEFKRCYDAN 600 L +GIPAA+VS+FLWERGLVVEKTGLYSFLVLFSMGITKGKWSTL+TELLEFKR YD N Sbjct: 541 LGARGIPAAVVSKFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLLTELLEFKRHYDGN 600 Query: 601 LPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAKAMKRMYTVLPEVAMRPSEA 660 PL LPSV A RY G+GLRDL D +H YR NATAK +KR++T LPEVA+ P++A Sbjct: 601 TPLSSCLPSVGAADALRYQGMGLRDLCDQLHDCYRANATAKQLKRLFTRLPEVAVSPAQA 660 Query: 661 YDKLVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMPGERFTEATRSILDYLEFARTFE 720 YDK+VRGEVEAVPI L GR+AAVMLVPYPPGIPLIMPGERFTEATRSILDYL FAR F Sbjct: 661 YDKMVRGEVEAVPIEALLGRVAAVMLVPYPPGIPLIMPGERFTEATRSILDYLAFARAFN 720 Query: 721 RAFPGFDSDVHGLQHQDGPSGRCYTVECIKE 751 + FPGF +DVHGLQH+ G YTV+CI E Sbjct: 721 QGFPGFVADVHGLQHEGGR----YTVDCITE 747 Lambda K H 0.320 0.136 0.407 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: 1685 Number of extensions: 53 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: 751 Length of database: 749 Length adjustment: 40 Effective length of query: 711 Effective length of database: 709 Effective search space: 504099 Effective search space used: 504099 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