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_3336 Lysine decarboxylase, inducible (EC 4.1.1.18)

Query= BRENDA::P28629
         (755 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3336
          Length = 751

 Score =  574 bits (1480), Expect = e-168
 Identities = 310/765 (40%), Positives = 452/765 (59%), Gaps = 36/765 (4%)

Query: 3   VLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGFAILSSNEAIDCLMFSYQ 62
           VLIV  + +  D+  G+ V  +A  L Q+  +V+ +  + +G  + S+   + C++ + +
Sbjct: 9   VLIVHRD-IKADSVAGDRVRGIARELEQEGFSVVSAVDYTEGRLVASTYHGLSCMLIASE 67

Query: 63  MEHPDEH--QNVRQLIGKLHERQQNVPVFLLGDR---EKALAAMDRDLLELVDEFAWILE 117
                 H  QN+ +LIG    R  ++P+F LG++   E A A    +L +L     ++ E
Sbjct: 68  DASTHSHLLQNMAELIGLARVRAPDLPIFALGEKVTLENAPADAMAELNQLRG-ILYLFE 126

Query: 118 DTADFIAGRAVAAMTRYRQQLLPPLFSALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFY 177
           DT  F+A +   A  +Y   LLPP F AL++++    YSW  PGH GGV + K+P G+ +
Sbjct: 127 DTVPFLARQVARAARKYLDGLLPPFFKALVQHTADSNYSWHTPGHGGGVAYHKSPVGQAF 186

Query: 178 HDYYGENLFRTDMGIERTSLGSLLDHTGAFGESEKYAARVFGADRSWSVVVGTSGSNRTI 237
           H ++GEN  R+D+ +    LGSLLDHTG   E+E  AAR FGAD ++ V+ GTS +N+ +
Sbjct: 187 HQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEARAARNFGADHTFFVINGTSTANKIV 246

Query: 238 MQACMTDNDVVVVDRNCHKSIEQGLMLTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQK 297
             + +  +D+V+VDRNCHKS+   +++TGA P+Y+ P RN  GIIGPI   E   E++Q 
Sbjct: 247 WHSVVARDDLVLVDRNCHKSVLHSIIMTGAIPLYLCPERNELGIIGPIPLSEFSRESIQA 306

Query: 298 KISESPLTKDKAGQKPSYCVVTNCTYDGVCYNAKEAQDLLEKTSDRLHFDEAWYGYARFN 357
           KI  SPLTK ++  K    VVTN TYDG+CYNA+  +  L  + + LHFDEAWY YA F+
Sbjct: 307 KIDASPLTKGRS-PKVKLAVVTNSTYDGLCYNAELIRQQLGNSVEVLHFDEAWYAYAAFH 365

Query: 358 PIYADHYAMRGEPGDHNGPTVFATHSTHKLLNALSQASYIHVREGRGA-INFSRFNQAYM 416
             +A  Y M G   D + P VF THSTHKLL A SQAS IHVR+G    ++  RFN+A+M
Sbjct: 366 EFFAGRYGM-GTSRDEDSPLVFTTHSTHKLLAAFSQASMIHVRDGGARQLDRDRFNEAFM 424

Query: 417 MHATTSPLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTADGSWFF 476
           MH +TSP Y I AS DVA +MM+G +G SL QE+ DEA+ FR+A+A L +   AD  W+F
Sbjct: 425 MHISTSPQYGIIASLDVASAMMEGPAGRSLLQEMFDEALSFRRALANLRQHIAAD-DWWF 483

Query: 477 KPWNKEVVTDPQTGKTYDFADAPTKLLTTVQDCWVMHPGESWHGFKDIPDNWSMLDPIKV 536
             W       P + +  +           V + W++ P   WHGF  + D++ +LDPIKV
Sbjct: 484 SIWQ------PPSAEGIE---------RVVTEDWLLQPDADWHGFGGVTDDYVLLDPIKV 528

Query: 537 SILAPGMGEDGELEETGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLVN 596
           +++ PG+   G L E G+PAA+V+ +L   G+V  +T  +  + LFSMG+T+GKW TL+ 
Sbjct: 529 TLVMPGLTAGGALSERGIPAAVVSKFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLLT 588

Query: 597 TLCSFKRHYDANTPLAQVMPELVEQYPDTYANMGIHDLGDTMFAWLKENNPGARLNEAYS 656
            L  FKR YDAN  LA  +P + ++    Y  MG+ DL D + A  + N     L   Y+
Sbjct: 589 ELLEFKRSYDANVSLASCLPCVAQENVARYQGMGLRDLCDQLHACYRSNATARHLKRMYT 648

Query: 657 GLPVAEVTPREAYNAIVDNNVELVSIENLPGRIAANSVIPYPPGIPMLLSGENFGDKNSP 716
            LP   + P +AY+ +V   VE VSI+ L GRIAA  ++PYPPGIP+++ GE F +    
Sbjct: 649 VLPEVAMKPADAYDQLVRGEVEAVSIDALDGRIAAVMLVPYPPGIPLIMPGERFTESTRS 708

Query: 717 QVSYLRSLQSWDHHFPGF-------EHETEGTEIIDGIYHVMCVK 754
            + YL   +++D  FPGF       +HE +G+      Y V C+K
Sbjct: 709 IIDYLAFARAFDSSFPGFVADVHGLQHEDQGS---GRCYTVDCIK 750


Lambda     K      H
   0.319    0.135    0.414 

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: 1380
Number of extensions: 60
Number of successful extensions: 6
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: 755
Length of database: 751
Length adjustment: 40
Effective length of query: 715
Effective length of database: 711
Effective search space:   508365
Effective search space used:   508365
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 (21.7 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