Alignments for a candidate for cadA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for cadA in Pseudomonas simiae WCS417

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate GFF2401 PS417_12240 lysine decarboxylase

Query= SwissProt::Q9I2S7
         (751 letters)



>FitnessBrowser__WCS417:GFF2401
          Length = 751

 Score = 1270 bits (3287), Expect = 0.0
 Identities = 623/750 (83%), Positives = 679/750 (90%)

Query: 1   MYKDLKFPVLIVHRDIKADTVAGERVRGIAHELEQDGFSILSTASSAEGRIVASTHHGLA 60
           MYKDLKFPVLIVHRDIKADTVAG+RVRGIA ELEQ+GFSI S    AEGR+VASTHHGLA
Sbjct: 1   MYKDLKFPVLIVHRDIKADTVAGDRVRGIARELEQEGFSIFSAVDYAEGRLVASTHHGLA 60

Query: 61  CILVAAEGAGENQRLLQDVVELIRVARVRAPQLPIFALGEQVTIENAPAESMADLHQLRG 120
           C+L+AAEGAGEN  LLQ++VELIR+AR+RAP LPIFALGEQVT+ENAPA++M++L+QLRG
Sbjct: 61  CMLIAAEGAGENTHLLQNMVELIRLARLRAPNLPIFALGEQVTLENAPADAMSELNQLRG 120

Query: 121 ILYLFEDTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYRKS 180
           ILYLFEDTVPFLARQVARAAR YL GLLPPFF+ALV+HTA SNYSWHTPGHGGGVAYRKS
Sbjct: 121 ILYLFEDTVPFLARQVARAARTYLDGLLPPFFKALVQHTADSNYSWHTPGHGGGVAYRKS 180

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

Query: 241 TANKIVWHSMVGREDLVLVDRNCHKSILHSIIMTGAIPLYLTPERNELGIIGPIPLSEFS 300
           TANKIVWHSMVGR+DLVLVDRNCHKS+LHSIIMTGAIPLYL PERNELGIIGPIPLSEFS
Sbjct: 241 TANKIVWHSMVGRDDLVLVDRNCHKSVLHSIIMTGAIPLYLCPERNELGIIGPIPLSEFS 300

Query: 301 KQSIAAKIAASPLARGREPKVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFDEAWYA 360
            +SI AKI ASPL RGR PKVKLAVVTNSTYDGLCYNAELIKQ LG+SVEVLHFDEAWYA
Sbjct: 301 PESIRAKIDASPLTRGRPPKVKLAVVTNSTYDGLCYNAELIKQQLGNSVEVLHFDEAWYA 360

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

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

Query: 481 WWFGVWQPEQVEGTDQVGTHDWVLEPSADWHGFGDIAEDYVLLDPIKVTLTTPGLSAGGK 540
           WWF +WQP  V G D+V T DW+L P  DWHGFGD+AEDYVLLDPIKVTL  PGL+AGG 
Sbjct: 481 WWFSIWQPPSVAGIDRVVTADWLLHPQDDWHGFGDVAEDYVLLDPIKVTLVMPGLTAGGA 540

Query: 541 LSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLVTELLEFKRCYDAN 600
           LS+ GIPAA+VS+FLWERGLVVEKTGLYSFLVLFSMGITKGKWSTL+TELLEFKR YDAN
Sbjct: 541 LSDCGIPAAVVSKFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLLTELLEFKRSYDAN 600

Query: 601 LPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAKAMKRMYTVLPEVAMRPSEA 660
           + L   LPSV   G  RY G+GLRDL D +H+ YR NATAK +KRMYTVLPE+AM+P++A
Sbjct: 601 VSLASCLPSVFAQGPTRYQGLGLRDLCDQLHSCYRSNATAKHLKRMYTVLPEIAMKPADA 660

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

Query: 721 RAFPGFDSDVHGLQHQDGPSGRCYTVECIK 750
            +FPGF +DVHGLQH+D  SGRCYTV+CIK
Sbjct: 721 SSFPGFVADVHGLQHEDDGSGRCYTVDCIK 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: 1727
Number of extensions: 56
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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Candidates (tab-delimited)
Steps (tab-delimited)
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Protein sequences (fasta format)
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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 (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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources