GapMind for catabolism of small carbon sources

 

Alignments 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.

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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:

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:

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:

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:

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