Aligments for a candidate for odc in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Aligments for a candidate for odc in Acidovorax sp. GW101-3H11

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate Ac3H11_2914 Arginine decarboxylase (EC 4.1.1.19); Ornithine decarboxylase (EC 4.1.1.17); Lysine decarboxylase (EC 4.1.1.18)

Query= BRENDA::Q5ZH57
         (745 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2914
          Length = 761

 Score =  365 bits (937), Expect = e-105
 Identities = 223/629 (35%), Positives = 335/629 (53%), Gaps = 26/629 (4%)

Query: 113 REIEAAAKKYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGEN 172
           R I   AK Y + V PPFFKAL  Y E G+  + CPGH GG  F KSP G+ ++ FYGEN
Sbjct: 134 RHIIREAKSYLESVQPPFFKALLDYAEDGSYSWHCPGHSGGVAFLKSPVGQMYHQFYGEN 193

Query: 173 IFRSDICNADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAP 232
           + R+D+CNA  +LG LL H G   ++E++AAR+FNAD  +FV NGT+TSN +     VAP
Sbjct: 194 MLRADVCNAVEELGQLLDHNGAIGESERNAARIFNADHCFFVTNGTSTSNKMVWHHTVAP 253

Query: 233 GDLVLFDRNNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKIAKVD 292
           GD+V+ DRN HKS+ + +++  G  PV+++ +R+ +G IG I   +F+  +I+ KI K +
Sbjct: 254 GDVVVVDRNCHKSILH-SIIMTGAIPVFMKPTRNHFGIIGPIPQSEFEPAAIQAKI-KAN 311

Query: 293 P----EKAKAKRPFRLAVIQLGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIPM 348
           P      AK  +P R+  +   TYDG +YN + +   +    D + FD AW+ +  F P 
Sbjct: 312 PLLKGVDAKKVKP-RVLTLTQSTYDGVLYNTETIKGMLDGYVDNLHFDEAWLPHAAFHPF 370

Query: 349 MKDSSPL-LLNLGPDDPGILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNA 407
                 +      P       TQS HK  AG SQAS +  +DS      R++    FN A
Sbjct: 371 YGSYHAMGKKRTRPKYSVTYATQSIHKLLAGISQASHVLVQDSQTAKLDRHL----FNEA 426

Query: 408 YMKFSSTSPFYPLFATLDINAKMQEGEAGKKLWHDALVTSVNARKNLL-------KNATM 460
           Y+  +STSP Y + A+ D+ A M E   G  L  ++L+ +++ R+ +        KN   
Sbjct: 427 YLMHTSTSPQYSIIASCDVAAAMMEPPGGTALVEESLLEALDFRRAMRQVEEDFGKNDWW 486

Query: 461 IKPFLPPVVHGKPWQDADTEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTP 520
            K + P  +  +    A+   I SD    K   G+KWHGF   AD    +DP K  + TP
Sbjct: 487 FKVWGPDKLVDEGLGRAEDWIIRSDGKGKK--NGSKWHGFGQLADGFNMLDPIKSTIVTP 544

Query: 521 GIDVETGEYEDFGIPAVILANYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVK 580
           G++++ G+++  GIPA I+  YL EHG++ EK  L S   + T   T+ + + L+T + +
Sbjct: 545 GLNLD-GKFDKTGIPASIVTKYLAEHGVVVEKTGLYSFFIMFTIGITKGRWNTLLTALQQ 603

Query: 581 FESLVKADAPLDEVLPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYF 640
           F+   + + P+  +LP    +H+ RYE   ++ LCQ VH+ Y   +      EM+L    
Sbjct: 604 FKDDYEKNQPMWRILPEFCQQHK-RYERMGLRDLCQHVHEMYAKYDIARLTTEMYLSDLT 662

Query: 641 PEQAMTPYQANVELLKNNAKLVPLTDIEGLAALEGALPYPPGIFCIVPGEKWTKVAQKYF 700
           P  AM P  A   +     + V + ++EG   +    PYPPGI  ++PGE + K    Y 
Sbjct: 663 P--AMKPSDAYAHIAHRTTERVEIDNLEGRITVGLVTPYPPGIPLLIPGEVFNKKIVDYL 720

Query: 701 LILEESINRFPGFAPEIQG-VYFEKENGK 728
               E     PGF  +I G V  E E+G+
Sbjct: 721 KFAREFAKLCPGFETDIHGLVEVEDESGQ 749


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: 1324
Number of extensions: 61
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 745
Length of database: 761
Length adjustment: 40
Effective length of query: 705
Effective length of database: 721
Effective search space:   508305
Effective search space used:   508305
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, or view the source code.

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