Alignments for a candidate for cadA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for cadA in Pseudomonas fluorescens GW456-L13

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate PfGW456L13_3776 Arginine decarboxylase (EC 4.1.1.19) / Ornithine decarboxylase (EC 4.1.1.17)

Query= SwissProt::Q9I2S7
         (751 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3776
          Length = 761

 Score =  636 bits (1640), Expect = 0.0
 Identities = 331/737 (44%), Positives = 464/737 (62%), Gaps = 24/737 (3%)

Query: 20  TVAGERVRGIAHELEQDGFSILSTASSAEGRIVASTHHGLACILVAAEGAGENQRLLQDV 79
           TV G  +  + H++E  G S+L++ S  +   +  +   + C+L+  E   +      D 
Sbjct: 23  TVFGRALDQLVHDVEGRGVSVLASESLTDAASILRSDPAIQCVLIRWEM--DTSEGHADC 80

Query: 80  VELIRVARVRAPQLPIFALGEQVTIENAPAESMADLHQLRGILYLFEDTVPFLARQVARA 139
            +L+   R R  ++P+F + ++ T  + P   +  +      ++L EDT  FL+ ++  A
Sbjct: 81  TKLLVKLRERNTRVPVFLISDRTTASSIP---LLVMQHADDFIWLPEDTSRFLSGRILAA 137

Query: 140 ARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYRKSPVGQAFHQFFGENTLRSDL 199
              Y    LPP F ALV+      YSWHTPGH GG A+ KS  G+AF++FFGEN LRSDL
Sbjct: 138 IERYRQAALPPMFGALVKFARNYEYSWHTPGHAGGTAFLKSTAGRAFYEFFGENLLRSDL 197

Query: 200 SVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVINGTSTANKIVWHSMVGREDLVLV 259
           S+SV ELGSLLDH+GP+ + E  AA+ FGA  T++V NG+S +N+++  + V R  + L 
Sbjct: 198 SISVGELGSLLDHSGPIGQGERYAAKVFGAHRTYYVTNGSSMSNRVILMASVTRNQIALC 257

Query: 260 DRNCHKSILHSIIMTGAIPLYLTPERNELGIIGPIPLSEFSKQSIAAKIAASPLAR-GRE 318
           DRNCHKS  H++ ++GAIP YL P RN  GIIGPI     S + + A IA +PL + G +
Sbjct: 258 DRNCHKSAEHAMTLSGAIPTYLVPTRNRYGIIGPILPQTLSAEGVKAAIANNPLVKQGID 317

Query: 319 PKVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFDEAWYAYAAFHEFYDGRYGMGTSR 378
           P    A+VTNSTYDGL YN   +++ LG+SV+ LHFDEAWY YA F+  Y GR+ M  + 
Sbjct: 318 PTPVHAIVTNSTYDGLTYNVTRVEELLGESVDRLHFDEAWYGYARFNPLYSGRHAMHGNP 377

Query: 379 SEEG---PLVFATHSTHKMLAAFSQASMIHVQDGGTRKLDVARFNEAFMMHISTSPQYGI 435
           ++     P VFAT STHK+LAA SQASMIHV+DG    ++ ARFNE++MMH STSP Y I
Sbjct: 378 ADHDKSKPTVFATQSTHKLLAALSQASMIHVRDG-RNPIEHARFNESYMMHASTSPNYAI 436

Query: 436 IASLDVASAMMEGPAGRSLIQETFDEALSFRRALANVRQNL-DRNDWWFGVWQPEQVE-G 493
           +AS DV+SAMME P+G+ L  E+ +EA+SFR+ L+ +   +  +NDW+F  WQP  V+ G
Sbjct: 437 MASCDVSSAMMEAPSGQILTNESIEEAISFRQVLSRMHNEMVGKNDWFFTCWQPPTVQVG 496

Query: 494 TDQVGTHD------------WVLEPSADWHGFGDIAEDYVLLDPIKVTLTTPGLSAGGKL 541
              V  H+            WVL P+A WHGFGDI + Y +LDPIKV++ +PG+   G L
Sbjct: 497 AAAVPFHEVDPATLKTDPNCWVLHPNAVWHGFGDIEDGYCMLDPIKVSVLSPGMGDDGSL 556

Query: 542 SEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLVTELLEFKRCYDANL 601
              GIPA +V+ +L  +G+VVEKT  ++ L LFS+GITKGKW TL+  LL+FKR YD N 
Sbjct: 557 LASGIPACVVTAYLGRQGIVVEKTTDFTILFLFSIGITKGKWGTLLNALLDFKRDYDDNA 616

Query: 602 PLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAKAMKRMYTVLPEVAMRPSEAY 661
            L   LP +  A   RY G+GL+DL+D + A+ + + T   M + +  LP+    P EAY
Sbjct: 617 ELELCLPDLYNANQHRYAGMGLKDLADEIFAAMKKHKTTANMSQAFGTLPKAEFSPVEAY 676

Query: 662 DKLVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMPGERFTEATRSILDYLEFARTFER 721
           +KLVR ++E V +    GR+AA  +VPYPPGIPL+MPGE    A   +L YL+    F++
Sbjct: 677 EKLVRNDIELVTLNEAAGRLAATGIVPYPPGIPLLMPGENAGPADGPLLAYLKALEAFDK 736

Query: 722 AFPGFDSDVHGLQHQDG 738
           +FPGF  D HG++ +DG
Sbjct: 737 SFPGFTHDTHGIEVEDG 753


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: 1446
Number of extensions: 53
Number of successful extensions: 7
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: 761
Length adjustment: 40
Effective length of query: 711
Effective length of database: 721
Effective search space:   512631
Effective search space used:   512631
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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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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