Aligments for a candidate for odc in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Aligments for a candidate for odc in Pseudomonas fluorescens GW456-L13

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

Query= BRENDA::Q5ZH57
         (745 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3776 Arginine
           decarboxylase (EC 4.1.1.19) / Ornithine decarboxylase
           (EC 4.1.1.17)
          Length = 761

 Score =  350 bits (898), Expect = e-100
 Identities = 222/679 (32%), Positives = 333/679 (49%), Gaps = 30/679 (4%)

Query: 65  IINKADETKFNIPIFIITDDSSKVDGETMSKIFHIID--WHNNYDRRLYDREIEAAAKKY 122
           ++ K  E    +P+F+I+D ++      +  + H  D  W      R     I AA ++Y
Sbjct: 83  LLVKLRERNTRVPVFLISDRTT-ASSIPLLVMQHADDFIWLPEDTSRFLSGRILAAIERY 141

Query: 123 EDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGENIFRSDICNAD 182
               LPP F AL  +       +  PGH GG  F KS AGR FY F+GEN+ RSD+  + 
Sbjct: 142 RQAALPPMFGALVKFARNYEYSWHTPGHAGGTAFLKSTAGRAFYEFFGENLLRSDLSISV 201

Query: 183 VDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAPGDLVLFDRNN 242
            +LG LL H GP    E++AA+VF A +TY+V NG++ SN + + A+V    + L DRN 
Sbjct: 202 GELGSLLDHSGPIGQGERYAAKVFGAHRTYYVTNGSSMSNRVILMASVTRNQIALCDRNC 261

Query: 243 HKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKIAKVDPEKAKAKRPF 302
           HKS  + A+  +G  P YL  +R+ YG IG I  +    + ++  IA     K       
Sbjct: 262 HKSAEH-AMTLSGAIPTYLVPTRNRYGIIGPILPQTLSAEGVKAAIANNPLVKQGIDPTP 320

Query: 303 RLAVIQLGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIPMMKDSSPLLLNLGPD 362
             A++   TYDG  YN  +V E +G   D + FD AW GY +F P+      +  N    
Sbjct: 321 VHAIVTNSTYDGLTYNVTRVEELLGESVDRLHFDEAWYGYARFNPLYSGRHAMHGNPADH 380

Query: 363 D---PGILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNAYMKFSSTSPFYP 419
           D   P +  TQSTHK  A  SQAS IH +D      +  I H +FN +YM  +STSP Y 
Sbjct: 381 DKSKPTVFATQSTHKLLAALSQASMIHVRDG-----RNPIEHARFNESYMMHASTSPNYA 435

Query: 420 LFATLDINAKMQEGEAGKKLWHDALVTSVNARKNLL--------KNATMIKPFLPPVVH- 470
           + A+ D+++ M E  +G+ L ++++  +++ R+ L         KN      + PP V  
Sbjct: 436 IMASCDVSSAMMEAPSGQILTNESIEEAISFRQVLSRMHNEMVGKNDWFFTCWQPPTVQV 495

Query: 471 ---GKPWQDADTEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTPGIDVETG 527
                P+ + D   + +D + W     A WHGF    D    +DP K  + +PG+  + G
Sbjct: 496 GAAAVPFHEVDPATLKTDPNCWVLHPNAVWHGFGDIEDGYCMLDPIKVSVLSPGMG-DDG 554

Query: 528 EYEDFGIPAVILANYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVKFESLVKA 587
                GIPA ++  YL   GI+ EK    +ILFL +   T+ K   L+  ++ F+     
Sbjct: 555 SLLASGIPACVVTAYLGRQGIVVEKTTDFTILFLFSIGITKGKWGTLLNALLDFKRDYDD 614

Query: 588 DAPLDEVLPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYFPEQAMTP 647
           +A L+  LP LY+ +Q RY G  +K L  E+    K + T     + F     P+   +P
Sbjct: 615 NAELELCLPDLYNANQHRYAGMGLKDLADEIFAAMKKHKTTANMSQAF--GTLPKAEFSP 672

Query: 648 YQANVELLKNNAKLVPLTDIEGLAALEGALPYPPGIFCIVPGEKWTKV---AQKYFLILE 704
            +A  +L++N+ +LV L +  G  A  G +PYPPGI  ++PGE           Y   LE
Sbjct: 673 VEAYEKLVRNDIELVTLNEAAGRLAATGIVPYPPGIPLLMPGENAGPADGPLLAYLKALE 732

Query: 705 ESINRFPGFAPEIQGVYFE 723
                FPGF  +  G+  E
Sbjct: 733 AFDKSFPGFTHDTHGIEVE 751


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: 1233
Number of extensions: 62
Number of successful extensions: 9
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: 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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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, 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