GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Cupriavidus basilensis 4G11

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate RR42_RS28050 RR42_RS28050 3-hydroxypropionyl-CoA dehydratase

Query= BRENDA::P76082
         (255 letters)



>FitnessBrowser__Cup4G11:RR42_RS28050
          Length = 261

 Score =  149 bits (377), Expect = 4e-41
 Identities = 94/251 (37%), Positives = 134/251 (53%), Gaps = 6/251 (2%)

Query: 7   SRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITG-NARFFAAGADL 65
           S +  +  LTL+ P   N +   L   L   L+A A D ++   V+TG   R F AG+D+
Sbjct: 12  SAKDGIATLTLDNPPL-NVVFRGLTEALDRALDALARDPAVRAVVLTGAGTRAFCAGSDI 70

Query: 66  NE----MAEKDLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGE 121
            E    M    +       +  ++ RL  F KP +AAVNG A G G E+A+ CD++VA E
Sbjct: 71  AEFRPLMRPGQIVPGKLALQHAVFGRLDDFPKPTVAAVNGLAFGGGLEIAVCCDLIVADE 130

Query: 122 NARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSD 181
            ARF LPEI LG+ PG+GG  R+ R VG+  A +++  GE I A  A   GLV+ V P  
Sbjct: 131 TARFALPEIKLGVFPGSGGPVRVTRRVGEGRAKELMFLGEPIDAATALAWGLVNRVAPPG 190

Query: 182 LTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGI 241
             L+ AL LA+ +AR  PLAL   KQA+  S +      + Q   L   + ++++  EG+
Sbjct: 191 QALQAALALAATLARRPPLALALCKQAIDLSFDTTEDEAMRQALPLSDRVFSSKEAQEGV 250

Query: 242 SAFLQKRTPDF 252
            AF  + TP F
Sbjct: 251 RAFFARETPRF 261


Lambda     K      H
   0.318    0.130    0.356 

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: 131
Number of extensions: 4
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: 255
Length of database: 261
Length adjustment: 24
Effective length of query: 231
Effective length of database: 237
Effective search space:    54747
Effective search space used:    54747
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 (21.8 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