GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaG in Pseudomonas fluorescens FW300-N2C3

Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate AO356_26360 AO356_26360 enoyl-CoA hydratase

Query= BRENDA::P77467
         (262 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_26360
          Length = 257

 Score =  139 bits (351), Expect = 5e-38
 Identities = 91/263 (34%), Positives = 144/263 (54%), Gaps = 12/263 (4%)

Query: 3   EFILSHVEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCA 62
           E IL  ++  V  +TLNRP+ LN+ N ++ ++L + L  +E D  I C++LTG+ + F A
Sbjct: 4   ETILLEIKDRVGLITLNRPQALNALNAQIVSELNQALDSLEADPKIGCIVLTGSKKAFAA 63

Query: 63  GQDLNDRNVDPTGPA---PDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLAL 119
           G D+ +   + T P     DL    +R  N   RR     KP+I AVNG A G G  LAL
Sbjct: 64  GADIKEM-AELTYPQIYLDDLFSDSDRVAN---RR-----KPIIAAVNGFALGGGCELAL 114

Query: 120 GGDIVIAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWG 179
             D ++A  +AKF      LG++P  GGT  L R  G+A+AM + L G  + A +A   G
Sbjct: 115 MCDFILAGDNAKFGQPEINLGVLPGMGGTQRLTRAVGKAKAMEMCLTGRFIDAVEAERCG 174

Query: 180 MIWQVVDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAG 239
           ++ ++V  + L D A + A  +A++      ++K+++N A   +L   +  ER     A 
Sbjct: 175 IVARIVPADELLDDALKTAALIASKSVPISMMVKESVNRAFEVSLSEGVRFERRVFHAAF 234

Query: 240 RSADYREGVSAFLAKRSPQFTGK 262
            + D +EG++AF+AKR+ +F  K
Sbjct: 235 ATQDQKEGMAAFVAKRAAEFQDK 257


Lambda     K      H
   0.321    0.136    0.403 

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: 129
Number of extensions: 8
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: 262
Length of database: 257
Length adjustment: 24
Effective length of query: 238
Effective length of database: 233
Effective search space:    55454
Effective search space used:    55454
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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