Aligments for a candidate for pcaD in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for pcaD in Pseudomonas simiae WCS417

Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate GFF1326 PS417_06740 4-carboxymuconolactone decarboxylase

Query= BRENDA::Q0SH24
         (400 letters)



>FitnessBrowser__WCS417:GFF1326
          Length = 132

 Score =  119 bits (298), Expect = 5e-32
 Identities = 56/118 (47%), Positives = 78/118 (66%)

Query: 269 HAQGMTVRRSILGDAHVDRSVAGTTDFTAPFQDFITRTAWGDIWSRPGLDHELRRLLTIA 328
           +A+G+ VRR +LGDAHVDRS+   T+F + FQ+ ITR AWGDIW+RPGL    R L+TIA
Sbjct: 7   YAEGLQVRREVLGDAHVDRSLNALTEFNSEFQEMITRHAWGDIWTRPGLPRHTRSLITIA 66

Query: 329 VLTAVGNEHELDMHIRAALRAGVDADTIGEVLLHTSVYAGVPNSNLGFALGKQALADL 386
           +L  +    EL +H+RAA   GV    I EVL+ +++Y G+P +N  F L +    +L
Sbjct: 67  MLIGMNRSEELKLHLRAAASNGVTRAEIKEVLMQSAIYCGIPAANATFHLAESVWDEL 124


Lambda     K      H
   0.318    0.132    0.392 

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: 121
Number of extensions: 5
Number of successful extensions: 1
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: 400
Length of database: 132
Length adjustment: 22
Effective length of query: 378
Effective length of database: 110
Effective search space:    41580
Effective search space used:    41580
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: 46 (22.3 bits)

Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate GFF4008 PS417_20530 3-oxoadipate enol-lactonase

Query= BRENDA::Q0SH24
         (400 letters)



>FitnessBrowser__WCS417:GFF4008
          Length = 267

 Score =  113 bits (283), Expect = 6e-30
 Identities = 77/240 (32%), Positives = 118/240 (49%), Gaps = 9/240 (3%)

Query: 22  VVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDGPYSVRDLSEDVLALLDS 81
           ++L+  LGS+   W+ QI  L+   R++ VD RGHG S  P   YS++  + D+LAL++ 
Sbjct: 22  LILIHGLGSSSQDWELQIPVLARHYRLIVVDVRGHGRSDKPRERYSIQGFTLDLLALIEH 81

Query: 82  LGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGEPQA-----WIERAAASR 136
           L + AAH VGLSMGG IA  L    P +V SL ++ +A +     A     W +R + +R
Sbjct: 82  LDLPAAHVVGLSMGGMIAFQLAVDEPAQVKSLCIVNSAPEVKVRSADDYWQWAKRWSLAR 141

Query: 137 TDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCDALADWDFTADLS 196
                ++  A+  R F +    +  +  R   E  A      Y A  DA+  W     LS
Sbjct: 142 VLSLATIGKALGDRLFPK---PQQADLRRKMAERWAKNDKRAYLASFDAIVGWGVQERLS 198

Query: 197 RISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANLEQAGAVTALLREHI 256
           RI+ PTLVI+ + D  TP +  +     +  AR  V+  + H   L+Q     A L + +
Sbjct: 199 RITCPTLVISADHD-YTPVAQKENYVKLLPNARLVVIEDSRHATPLDQPEVFNATLLDFL 257


Lambda     K      H
   0.318    0.132    0.392 

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: 233
Number of extensions: 11
Number of successful extensions: 2
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: 400
Length of database: 267
Length adjustment: 28
Effective length of query: 372
Effective length of database: 239
Effective search space:    88908
Effective search space used:    88908
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: 48 (23.1 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