GapMind for catabolism of small carbon sources

 

Aligments for a candidate for cadA in Pseudomonas fluorescens FW300-N2E3

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate AO353_23560 AO353_23560 lysine decarboxylase

Query= SwissProt::Q9I2S7
         (751 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_23560 AO353_23560 lysine
           decarboxylase
          Length = 751

 Score = 1269 bits (3284), Expect = 0.0
 Identities = 621/750 (82%), Positives = 682/750 (90%)

Query: 1   MYKDLKFPVLIVHRDIKADTVAGERVRGIAHELEQDGFSILSTASSAEGRIVASTHHGLA 60
           MYKDLKFPVLIVHRDIKADTVAG+RVRGIA EL Q+GFS+LS     EGR+VASTHHGLA
Sbjct: 1   MYKDLKFPVLIVHRDIKADTVAGDRVRGIATELSQEGFSVLSAVDYTEGRLVASTHHGLA 60

Query: 61  CILVAAEGAGENQRLLQDVVELIRVARVRAPQLPIFALGEQVTIENAPAESMADLHQLRG 120
           C+L+AAEGAGEN  LLQ++ ELIRVAR RAP LPIFALGEQVT+ENAPA++M++L+QLRG
Sbjct: 61  CMLIAAEGAGENIHLLQNMAELIRVARARAPNLPIFALGEQVTLENAPADAMSELNQLRG 120

Query: 121 ILYLFEDTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYRKS 180
           ILYLFEDTVPFLARQVARAAR+YL GLLPPFF+ALV+HTA SNYSWHTPGHGGGVAY KS
Sbjct: 121 ILYLFEDTVPFLARQVARAARSYLDGLLPPFFKALVQHTADSNYSWHTPGHGGGVAYHKS 180

Query: 181 PVGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVINGTS 240
           PVGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAE RAARNFGADHTFFVINGTS
Sbjct: 181 PVGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEARAARNFGADHTFFVINGTS 240

Query: 241 TANKIVWHSMVGREDLVLVDRNCHKSILHSIIMTGAIPLYLTPERNELGIIGPIPLSEFS 300
           TANKIVW +MV R+DLVLVDRNCHKS+LHSIIMTGAIPLYL PERNELGIIGPIPLSEFS
Sbjct: 241 TANKIVWQAMVARDDLVLVDRNCHKSVLHSIIMTGAIPLYLCPERNELGIIGPIPLSEFS 300

Query: 301 KQSIAAKIAASPLARGREPKVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFDEAWYA 360
           ++SI AKI ASPL +GR PKVKLAVVTNSTYDGLCYNAELIKQTLG+SVEVLHFDEAWYA
Sbjct: 301 RESIQAKIDASPLTKGRTPKVKLAVVTNSTYDGLCYNAELIKQTLGNSVEVLHFDEAWYA 360

Query: 361 YAAFHEFYDGRYGMGTSRSEEGPLVFATHSTHKMLAAFSQASMIHVQDGGTRKLDVARFN 420
           YAAFHEF+ GRYGMGTSR+++ PLVF THSTHK+LAAFSQASMIHVQDGG R+LD  RFN
Sbjct: 361 YAAFHEFFAGRYGMGTSRTDDSPLVFTTHSTHKLLAAFSQASMIHVQDGGARQLDRDRFN 420

Query: 421 EAFMMHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALANVRQNLDRND 480
           EAFMMHISTSPQY IIASLDVASAMMEGPAGRSL+QE FDEALSFRRALAN+RQ++  +D
Sbjct: 421 EAFMMHISTSPQYSIIASLDVASAMMEGPAGRSLLQEMFDEALSFRRALANLRQHIATDD 480

Query: 481 WWFGVWQPEQVEGTDQVGTHDWVLEPSADWHGFGDIAEDYVLLDPIKVTLTTPGLSAGGK 540
           WWF +WQP  VEG D+V T DW+L+P ADWHGFGDIAEDYVLLDPIKVTL  PGL+AGG 
Sbjct: 481 WWFSIWQPPLVEGIDKVTTSDWLLQPEADWHGFGDIAEDYVLLDPIKVTLVMPGLTAGGA 540

Query: 541 LSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLVTELLEFKRCYDAN 600
           LSE+GIPAA+VS+FLWERGLVVEKTGLYSFLVLFSMGITKGKWSTL+TELLEFKR YDAN
Sbjct: 541 LSERGIPAAVVSKFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLLTELLEFKRSYDAN 600

Query: 601 LPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAKAMKRMYTVLPEVAMRPSEA 660
           + L   LP VAQ    RY G+GLRDL D +HA YR NATAK +KRMYTVLPE+AM+P++A
Sbjct: 601 VSLATCLPCVAQRDVARYQGMGLRDLCDQLHACYRSNATAKHLKRMYTVLPEIAMKPADA 660

Query: 661 YDKLVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMPGERFTEATRSILDYLEFARTFE 720
           YD+LVRGEVEAV I  L+GRIAAVMLVPYPPGIPLIMPGERFTE+TRSI+DYL FARTF 
Sbjct: 661 YDQLVRGEVEAVSIDNLQGRIAAVMLVPYPPGIPLIMPGERFTESTRSIIDYLAFARTFN 720

Query: 721 RAFPGFDSDVHGLQHQDGPSGRCYTVECIK 750
            +FPGF +DVHGLQH+D  +GRCYTV+CIK
Sbjct: 721 SSFPGFVADVHGLQHEDEGNGRCYTVDCIK 750


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: 1696
Number of extensions: 41
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: 751
Length adjustment: 40
Effective length of query: 711
Effective length of database: 711
Effective search space:   505521
Effective search space used:   505521
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.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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