GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Pseudomonas stutzeri RCH2

Align crotonase (EC 4.2.1.150) (characterized)
to candidate GFF3051 Psest_3109 Enoyl-CoA hydratase/carnithine racemase

Query= metacyc::MONOMER-13469
         (259 letters)



>FitnessBrowser__psRCH2:GFF3051
          Length = 272

 Score =  178 bits (451), Expect = 1e-49
 Identities = 106/255 (41%), Positives = 147/255 (57%), Gaps = 2/255 (0%)

Query: 6   IILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSG-KAFVAG 64
           + +EK G+ A IT+N P A N  +  +L  +   +  +  DD++YA++I+G G K F AG
Sbjct: 19  LTVEKHGHTALITINHPPA-NTWDRESLIGLKQVVEHLNHDDDIYALVISGQGEKFFSAG 77

Query: 65  ADIAEMKDLTAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIAS 124
           AD+    D      R+ +    + F  L +     IAAINGFALGGG E +L+CD+RIA 
Sbjct: 78  ADLKLFADGDRNRAREMARRFGEAFEALRDFRGVSIAAINGFALGGGLECALACDLRIAE 137

Query: 125 SKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEP 184
            +A+ G PE  +G+ P  GGTQ LA  +G G AK +I  G+ I AE ALRIGL+ +VVEP
Sbjct: 138 QQAQMGLPEASVGLLPCAGGTQALAWLVGEGWAKRMILCGERITAETALRIGLIEQVVEP 197

Query: 185 DKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFATEDRVEG 244
            +    A  L   I   +P+AVR  K  I+   Q    T  A E E F E F  ED +EG
Sbjct: 198 GQARGHALLLAARIARQSPVAVRAIKPLIDGARQRLPHTFGAAEREAFVELFEAEDTLEG 257

Query: 245 MTAFVEKRDKAFKNK 259
           + AF+EKRD  ++N+
Sbjct: 258 VNAFLEKRDPRWRNR 272


Lambda     K      H
   0.318    0.136    0.376 

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: 182
Number of extensions: 8
Number of successful extensions: 3
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: 259
Length of database: 272
Length adjustment: 25
Effective length of query: 234
Effective length of database: 247
Effective search space:    57798
Effective search space used:    57798
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: 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