GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Pseudomonas fluorescens FW300-N1B4

Align crotonase (EC 4.2.1.150) (characterized)
to candidate Pf1N1B4_4777 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4777
          Length = 270

 Score =  139 bits (350), Expect = 6e-38
 Identities = 91/260 (35%), Positives = 133/260 (51%), Gaps = 11/260 (4%)

Query: 8   LEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAGADI 67
           +E   N+A + +NRP+ +N++NAA   EI      I + D V  V+++G+GK F +G D+
Sbjct: 9   VELADNIAHVQINRPEKINSMNAAFWSEIIEIFQWIDDTDEVRVVVLSGAGKHFSSGIDL 68

Query: 68  AEMKDLTAVEGRKFS----VLGNKI------FRKLENLEKPVIAAINGFALGGGCELSLS 117
             M  +    G+  S    +L   I      F  ++N  KPV+AAI G+ LGG  +L  +
Sbjct: 69  MMMAGMLNELGKDVSRNARLLRRTILTLQASFNAVDNCRKPVLAAIQGYCLGGAIDLISA 128

Query: 118 CDIRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGL 177
           CD+R A+  A+F   E+ +G+    G  QRL R IG GM +EL YTG+   A+EA  IGL
Sbjct: 129 CDMRYAAEDAQFSIKEIDIGMAADVGTLQRLPRIIGDGMLRELAYTGRTFGADEARSIGL 188

Query: 178 VNKVV-EPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECF 236
           VN+V  +   LLE    +   I   +PIAV   K  I+      ID G+ Y A       
Sbjct: 189 VNRVYSDAASLLEGVMGIAREIAGKSPIAVTGTKEMISYMRDHRIDDGLEYVATWNAAML 248

Query: 237 ATEDRVEGMTAFVEKRDKAF 256
            + D    M A + K+   F
Sbjct: 249 QSTDLRVAMAAHMSKQKPEF 268


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: 155
Number of extensions: 7
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: 270
Length adjustment: 25
Effective length of query: 234
Effective length of database: 245
Effective search space:    57330
Effective search space used:    57330
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