Alignments for a candidate for adiA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Pseudomonas putida KT2440

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate PP_4140 PP_4140 lysine decarboxylase

Query= BRENDA::E8X9U7
         (756 letters)



>FitnessBrowser__Putida:PP_4140
          Length = 749

 Score =  558 bits (1438), Expect = e-163
 Identities = 295/756 (39%), Positives = 446/756 (58%), Gaps = 25/756 (3%)

Query: 5   LIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGYAILSANEAIDCLMFSYQM 64
           +++    +  D+  G  V  +A+ L Q    ++ +    +   + + +  + C++ + + 
Sbjct: 9   ILIVHRAIKADSVAGERVRGIAEELRQDGFAILAAADHAEARLVAATHHGLACMLIAAEG 68

Query: 65  EQPDEHL--SVRQLIGKLHERQQNVPVFLLGDR---EKATASLDRDLLELVDEFAWILED 119
              + HL  ++ +LI     R  N+P+F LG++   E A A    +L +L     ++ ED
Sbjct: 69  AGENTHLLQNMAELIRLARLRAPNLPIFALGEQVTLENAPAEAMSELNQLRG-ILYLFED 127

Query: 120 TADFIAGRAVAAMTRYRQQLLPPLFNALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFYH 179
           T  F+A +   A   Y   LLPP F AL++++    YSW  PGH GGV + K+P G+ +H
Sbjct: 128 TVPFLARQVARAAHTYLDGLLPPFFKALVQHTAQSNYSWHTPGHGGGVAYHKSPVGQAFH 187

Query: 180 DYYGENLFRSDMGIERTTLGSLLDHTGAFGESEKNAARVFGADRSWSVVVGTSGSNRTIM 239
            ++GEN  RSD+ +    LGSLLDHTG   E+E  AAR FGAD ++ V+ GTS +N+ + 
Sbjct: 188 QFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEARAARNFGADHTFFVINGTSTANKIVW 247

Query: 240 QACMTDNDVVVLDRNCHKSIEQGLILTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQKK 299
            A +  +D+V++DRNCHKS+   +I+TGA P+Y+ P RN  GIIGPI   E  PE +  K
Sbjct: 248 HAMVGRDDLVLVDRNCHKSVVHAIIMTGAIPLYLCPERNELGIIGPIPLSEFSPEAIAAK 307

Query: 300 ISASPLTKTKAGQKPSYSVVTNCTYDGVCYNAKEAQDLLAKTSDRIHFDEAWYGYARFNP 359
           I A+PL + + GQ+   +VVTN TYDG+CY+A   +  L  + + +HFDEAW+ YA F+ 
Sbjct: 308 IQANPLARDR-GQRIKLAVVTNSTYDGLCYHAGLIKQALGASVEVLHFDEAWFAYAAFHD 366

Query: 360 IYCDHYAMRGEPGDHNGPTVFATHSTHKLLNALSQASYIHVREG-RGAVNFSRFNQAYMM 418
            +   YAM G     + P VF+THSTHKLL A SQAS IHV++G R  ++  RFN+A+MM
Sbjct: 367 FFTGRYAM-GTACAADSPLVFSTHSTHKLLAAFSQASMIHVQDGARRQLDRDRFNEAFMM 425

Query: 419 HATTSPLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTDEGDWFFK 478
           H +TSP Y+I AS DVA +MM+G +G SL QE+ DEA+ FR+A+A L +E     DW+F 
Sbjct: 426 HISTSPQYSILASLDVASTMMEGPAGRSLLQEMFDEALSFRRALANL-REHIAAADWWFS 484

Query: 479 PWNKDVVTDPQTGKTYDFADAPAKLLATDQNCWVMRPGETWHGFKDLPDNWSMLDPIKVS 538
            W                A+   +L A D   W+++PG  WHGF ++  ++ +LDP+KV+
Sbjct: 485 IWQPPS------------AEGIPRLAAQD---WLLQPGAQWHGFGEVVTDYVLLDPLKVT 529

Query: 539 ILAPGMGDDGELEASGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLINT 598
           ++ PG+  DG L A G+PAA+V+ +L   G+V  +T  +  + LFSMG+T+GKW TL+  
Sbjct: 530 LVMPGLSADGVLGARGIPAAVVSKFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLLTE 589

Query: 599 LCSFKHHYDANTPLAQVMPELVQDYPDTYANMGIHDLGDKMFAWLRENNPGARLNAAYST 658
           L  FK HYD NTPL+  +P +       Y  MG+ DL D++    R N    +L   ++ 
Sbjct: 590 LLEFKRHYDGNTPLSSCLPSVGAADALRYQGMGLRDLCDQLHDCYRANATAKQLKRLFTR 649

Query: 659 LPVAEITPRDAYNAIVNNNIEMVAIENLPGRIAANSVIPYPPGIPMLLSGENFGDENSPQ 718
           LP   ++P  AY+ +V   +E V IE L GR+AA  ++PYPPGIP+++ GE F +     
Sbjct: 650 LPEVAVSPAQAYDKMVRGEVEAVPIEALLGRVAAVMLVPYPPGIPLIMPGERFTEATRSI 709

Query: 719 VGYLRSLQSWDHHFPGFEHETEGTEIIDGVYHVMCV 754
           + YL   ++++  FPGF  +  G +   G Y V C+
Sbjct: 710 LDYLAFARAFNQGFPGFVADVHGLQHEGGRYTVDCI 745


Lambda     K      H
   0.319    0.135    0.415 

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: 1403
Number of extensions: 72
Number of successful extensions: 8
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: 756
Length of database: 749
Length adjustment: 40
Effective length of query: 716
Effective length of database: 709
Effective search space:   507644
Effective search space used:   507644
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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Steps (tab-delimited)
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