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

GapMind for catabolism of small carbon sources

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

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate PfGW456L13_3776 Arginine decarboxylase (EC 4.1.1.19) / Ornithine decarboxylase (EC 4.1.1.17)

Query= BRENDA::E8X9U7
         (756 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3776
          Length = 761

 Score =  756 bits (1952), Expect = 0.0
 Identities = 364/743 (48%), Positives = 505/743 (67%), Gaps = 7/743 (0%)

Query: 16  TWVGNAVERLADALSQQNVTVIKSTSFDDGYAILSANEAIDCLMFSYQMEQPDEHLSVRQ 75
           T  G A+++L   +  + V+V+ S S  D  +IL ++ AI C++  ++M+  + H    +
Sbjct: 23  TVFGRALDQLVHDVEGRGVSVLASESLTDAASILRSDPAIQCVLIRWEMDTSEGHADCTK 82

Query: 76  LIGKLHERQQNVPVFLLGDREKATASLDRDLLELVDEFAWILEDTADFIAGRAVAAMTRY 135
           L+ KL ER   VPVFL+ DR  A+ S+   +++  D+F W+ EDT+ F++GR +AA+ RY
Sbjct: 83  LLVKLRERNTRVPVFLISDRTTAS-SIPLLVMQHADDFIWLPEDTSRFLSGRILAAIERY 141

Query: 136 RQQLLPPLFNALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFYHDYYGENLFRSDMGIER 195
           RQ  LPP+F AL+K++  +EYSW  PGH GG  F K+ AGR +++++GENL RSD+ I  
Sbjct: 142 RQAALPPMFGALVKFARNYEYSWHTPGHAGGTAFLKSTAGRAFYEFFGENLLRSDLSISV 201

Query: 196 TTLGSLLDHTGAFGESEKNAARVFGADRSWSVVVGTSGSNRTIMQACMTDNDVVVLDRNC 255
             LGSLLDH+G  G+ E+ AA+VFGA R++ V  G+S SNR I+ A +T N + + DRNC
Sbjct: 202 GELGSLLDHSGPIGQGERYAAKVFGAHRTYYVTNGSSMSNRVILMASVTRNQIALCDRNC 261

Query: 256 HKSIEQGLILTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQKKISASPLTKTKAGQKPS 315
           HKS E  + L+GA P Y+VP+RNRYGIIGPI PQ +  E ++  I+ +PL K      P 
Sbjct: 262 HKSAEHAMTLSGAIPTYLVPTRNRYGIIGPILPQTLSAEGVKAAIANNPLVKQGIDPTPV 321

Query: 316 YSVVTNCTYDGVCYNAKEAQDLLAKTSDRIHFDEAWYGYARFNPIYCDHYAMRGEPGDH- 374
           +++VTN TYDG+ YN    ++LL ++ DR+HFDEAWYGYARFNP+Y   +AM G P DH 
Sbjct: 322 HAIVTNSTYDGLTYNVTRVEELLGESVDRLHFDEAWYGYARFNPLYSGRHAMHGNPADHD 381

Query: 375 -NGPTVFATHSTHKLLNALSQASYIHVREGRGAVNFSRFNQAYMMHATTSPLYAICASND 433
            + PTVFAT STHKLL ALSQAS IHVR+GR  +  +RFN++YMMHA+TSP YAI AS D
Sbjct: 382 KSKPTVFATQSTHKLLAALSQASMIHVRDGRNPIEHARFNESYMMHASTSPNYAIMASCD 441

Query: 434 VAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTDEGDWFFKPWNKDVVTDPQTG-K 492
           V+ +MM+  SG  LT E I+EA+ FRQ ++R++ E   + DWFF  W    V   Q G  
Sbjct: 442 VSSAMMEAPSGQILTNESIEEAISFRQVLSRMHNEMVGKNDWFFTCWQPPTV---QVGAA 498

Query: 493 TYDFADAPAKLLATDQNCWVMRPGETWHGFKDLPDNWSMLDPIKVSILAPGMGDDGELEA 552
              F +     L TD NCWV+ P   WHGF D+ D + MLDPIKVS+L+PGMGDDG L A
Sbjct: 499 AVPFHEVDPATLKTDPNCWVLHPNAVWHGFGDIEDGYCMLDPIKVSVLSPGMGDDGSLLA 558

Query: 553 SGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLINTLCSFKHHYDANTPL 612
           SG+PA +VTA+LGR GIV  +TTDF I+FLFS+G+T+GKWGTL+N L  FK  YD N  L
Sbjct: 559 SGIPACVVTAYLGRQGIVVEKTTDFTILFLFSIGITKGKWGTLLNALLDFKRDYDDNAEL 618

Query: 613 AQVMPELVQDYPDTYANMGIHDLGDKMFAWLRENNPGARLNAAYSTLPVAEITPRDAYNA 672
              +P+L       YA MG+ DL D++FA ++++   A ++ A+ TLP AE +P +AY  
Sbjct: 619 ELCLPDLYNANQHRYAGMGLKDLADEIFAAMKKHKTTANMSQAFGTLPKAEFSPVEAYEK 678

Query: 673 IVNNNIEMVAIENLPGRIAANSVIPYPPGIPMLLSGENFGDENSPQVGYLRSLQSWDHHF 732
           +V N+IE+V +    GR+AA  ++PYPPGIP+L+ GEN G  + P + YL++L+++D  F
Sbjct: 679 LVRNDIELVTLNEAAGRLAATGIVPYPPGIPLLMPGENAGPADGPLLAYLKALEAFDKSF 738

Query: 733 PGFEHETEGTEIIDGVYHVMCVK 755
           PGF H+T G E+ DGVY ++ +K
Sbjct: 739 PGFTHDTHGIEVEDGVYRMLVLK 761


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: 1523
Number of extensions: 69
Number of successful extensions: 4
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: 761
Length adjustment: 40
Effective length of query: 716
Effective length of database: 721
Effective search space:   516236
Effective search space used:   516236
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)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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