Alignments for a candidate for odc in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for odc in Pseudomonas simiae WCS417

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate GFF2401 PS417_12240 lysine decarboxylase

Query= BRENDA::Q5ZH57
         (745 letters)



>FitnessBrowser__WCS417:GFF2401
          Length = 751

 Score =  380 bits (977), Expect = e-109
 Identities = 223/625 (35%), Positives = 336/625 (53%), Gaps = 32/625 (5%)

Query: 113 REIEAAAKKYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGEN 172
           R++  AA+ Y DG+LPPFFKAL  +    N  +  PGH GG  +RKSP G+ F+ F+GEN
Sbjct: 134 RQVARAARTYLDGLLPPFFKALVQHTADSNYSWHTPGHGGGVAYRKSPVGQAFHQFFGEN 193

Query: 173 IFRSDICNADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAP 232
             RSD+  +  +LG LL H GP  +AE  AAR F AD T+FV+NGT+T+N I   + V  
Sbjct: 194 TLRSDLSVSVPELGSLLDHTGPLAEAEARAARNFGADHTFFVINGTSTANKIVWHSMVGR 253

Query: 233 GDLVLFDRNNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKIAKVD 292
            DLVL DRN HKSV + +++  G  P+YL   R+  G IG I   +F  +SIR   AK+D
Sbjct: 254 DDLVLVDRNCHKSVLH-SIIMTGAIPLYLCPERNELGIIGPIPLSEFSPESIR---AKID 309

Query: 293 PEKAKAKRP--FRLAVIQLGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIPMMK 350
                  RP   +LAV+   TYDG  YNA+ + +++G+  + + FD AW  Y  F     
Sbjct: 310 ASPLTRGRPPKVKLAVVTNSTYDGLCYNAELIKQQLGNSVEVLHFDEAWYAYAAFHEFFA 369

Query: 351 DSSPLLLNLGPDDPGILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNAYMK 410
               +  +  PD P +  T STHK  A FSQAS IH +D    G  R ++  +FN A+M 
Sbjct: 370 GRYGMGTSRTPDSPLVFTTHSTHKLLAAFSQASMIHVQD----GGARQLDRDRFNEAFMM 425

Query: 411 FSSTSPFYPLFATLDINAKMQEGEAGKKLWHDALVTSV-------NARKNLLKNATMIKP 463
             STSP Y + A+LD+ + M EG AG+ L  +    ++       N R+++ +       
Sbjct: 426 HISTSPQYSIIASLDVASAMMEGPAGRSLLQEMFDEALSFRRALANLRQHIAEEDWWFSI 485

Query: 464 FLPPVVHGKPWQDADTEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTPGID 523
           + PP V G        +++V+    W       WHGF   A++   +DP K  L  PG+ 
Sbjct: 486 WQPPSVAG-------IDRVVT--ADWLLHPQDDWHGFGDVAEDYVLLDPIKVTLVMPGL- 535

Query: 524 VETGEYEDFGIPAVILANYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVKFES 583
              G   D GIPA +++ +L E G++ EK  L S L L +   T+ K   L+T++++F+ 
Sbjct: 536 TAGGALSDCGIPAAVVSKFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLLTELLEFKR 595

Query: 584 LVKADAPLDEVLPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYFPEQ 643
              A+  L   LP ++++   RY+G  ++ LC ++H  Y++N T ++ K M+     PE 
Sbjct: 596 SYDANVSLASCLPSVFAQGPTRYQGLGLRDLCDQLHSCYRSNATAKHLKRMY--TVLPEI 653

Query: 644 AMTPYQANVELLKNNAKLVPLTDIEGLAALEGALPYPPGIFCIVPGEKWTKVAQK---YF 700
           AM P  A  +L++   + V +  + G  A    +PYPPGI  I+PGE++T+  +    Y 
Sbjct: 654 AMKPADAYDQLVRGEVEAVSIDALPGRIAAVMLVPYPPGIPLIMPGERFTESTRSIIDYL 713

Query: 701 LILEESINRFPGFAPEIQGVYFEKE 725
                  + FPGF  ++ G+  E +
Sbjct: 714 AFARTFDSSFPGFVADVHGLQHEDD 738


Lambda     K      H
   0.318    0.136    0.405 

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: 1132
Number of extensions: 53
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: 745
Length of database: 751
Length adjustment: 40
Effective length of query: 705
Effective length of database: 711
Effective search space:   501255
Effective search space used:   501255
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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