Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate GFF2032 Psest_2075 Arginine/lysine/ornithine decarboxylases
Query= SwissProt::Q9I2S7 (751 letters) >FitnessBrowser__psRCH2:GFF2032 Length = 749 Score = 1261 bits (3264), Expect = 0.0 Identities = 621/751 (82%), Positives = 681/751 (90%), Gaps = 2/751 (0%) Query: 1 MYKDLKFPVLIVHRDIKADTVAGERVRGIAHELEQDGFSILSTASSAEGRIVASTHHGLA 60 MYKDLKFP+LIVHRDIKADTVAGERVRGIA ELE+DGF+IL TASS EGRIVASTHHGLA Sbjct: 1 MYKDLKFPILIVHRDIKADTVAGERVRGIASELERDGFNILPTASSNEGRIVASTHHGLA 60 Query: 61 CILVAAEGAGENQRLLQDVVELIRVARVRAPQLPIFALGEQVTIENAPAESMADLHQLRG 120 CILVAAEGAG+NQRLL DVVELIRVAR RAP+LPIFALGEQVTIENAPAE+MADL++LRG Sbjct: 61 CILVAAEGAGDNQRLLHDVVELIRVARRRAPRLPIFALGEQVTIENAPAEAMADLNELRG 120 Query: 121 ILYLFEDTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYRKS 180 +LYL+EDTVPFLARQVARAAR+YL LLPPFF ALV HT +SNYSWHTPGHGGGVAYRKS Sbjct: 121 LLYLYEDTVPFLARQVARAARSYLDDLLPPFFSALVRHTGESNYSWHTPGHGGGVAYRKS 180 Query: 181 PVGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVINGTS 240 PVGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGP+A AE RAARNFGADHTFFVINGTS Sbjct: 181 PVGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGPVAAAEARAARNFGADHTFFVINGTS 240 Query: 241 TANKIVWHSMVGREDLVLVDRNCHKSILHSIIMTGAIPLYLTPERNELGIIGPIPLSEFS 300 TANKIVWHSMV R+DLVLVDRNCHKSILH+IIMTGAIPLY++P RNELGIIGPIPL EF+ Sbjct: 241 TANKIVWHSMVARDDLVLVDRNCHKSILHAIIMTGAIPLYMSPTRNELGIIGPIPLEEFT 300 Query: 301 KQSIAAKIAASPLARGREPKVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFDEAWYA 360 ++SI AKIAA+PLARGR PKVKLAVVTNSTYDGLCYNA LIK+TL D+VEVLHFDEAWYA Sbjct: 301 RESIQAKIAANPLARGRPPKVKLAVVTNSTYDGLCYNANLIKRTLADNVEVLHFDEAWYA 360 Query: 361 YAAFHEFYDGRYGMGTSRSEEGPLVFATHSTHKMLAAFSQASMIHVQDGGTRKLDVARFN 420 YAAFHEFYDGRYGM T E+GPLVF THSTHK+LAAFSQASMIHV D TR+LD RFN Sbjct: 361 YAAFHEFYDGRYGMDT--REQGPLVFTTHSTHKLLAAFSQASMIHVLDSQTRQLDRDRFN 418 Query: 421 EAFMMHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALANVRQNLDRND 480 EAFMMHISTSPQYGI+ASLDVASAMMEGPAGRSLIQETFDEALSFRRALAN+RQ++D +D Sbjct: 419 EAFMMHISTSPQYGILASLDVASAMMEGPAGRSLIQETFDEALSFRRALANLRQHIDADD 478 Query: 481 WWFGVWQPEQVEGTDQVGTHDWVLEPSADWHGFGDIAEDYVLLDPIKVTLTTPGLSAGGK 540 WWF +WQP V+G + + T DW+LEP+ADWHGFG+IA+DYVLLDPIKVTL TPGL+A G Sbjct: 479 WWFSIWQPPLVDGAEALVTPDWLLEPTADWHGFGEIADDYVLLDPIKVTLVTPGLTASGA 538 Query: 541 LSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLVTELLEFKRCYDAN 600 L + GIPAA+VS+FLWERGLVVEKTGLYS LVLFSMGITKGKWSTL+TELLEFKR YDAN Sbjct: 539 LGKSGIPAAVVSKFLWERGLVVEKTGLYSMLVLFSMGITKGKWSTLLTELLEFKRHYDAN 598 Query: 601 LPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAKAMKRMYTVLPEVAMRPSEA 660 +PL++ LPS+A+ G Y G+GLRDL DA+HA Y +NATA+AM+RMYT LPE AM P++A Sbjct: 599 IPLVEALPSIARKGAATYAGMGLRDLCDALHACYCENATARAMRRMYTALPEPAMTPAQA 658 Query: 661 YDKLVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMPGERFTEATRSILDYLEFARTFE 720 YDKLVRGEVEAVPI LEGRIAAVMLVPYPPGIPLIMPGERFT TRSILDYL FAR F Sbjct: 659 YDKLVRGEVEAVPIEALEGRIAAVMLVPYPPGIPLIMPGERFTGETRSILDYLRFARDFA 718 Query: 721 RAFPGFDSDVHGLQHQDGPSGRCYTVECIKE 751 FPGFD+DVHGLQH+ G G YTV+CI+E Sbjct: 719 ERFPGFDADVHGLQHEVGVGGSSYTVDCIRE 749 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: 1735 Number of extensions: 54 Number of successful extensions: 2 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