GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpD in Azospirillum brasilense Sp245

Align 2-keto-4-pentenoate hydratase 2; EC 4.2.1.80; 2-hydroxypentadienoic acid hydratase 2 (uncharacterized)
to candidate AZOBR_RS15705 AZOBR_RS15705 2-keto-4-pentenoate hydratase

Query= curated2:Q49KF9
         (270 letters)



>FitnessBrowser__azobra:AZOBR_RS15705
          Length = 254

 Score = 67.8 bits (164), Expect = 2e-16
 Identities = 60/204 (29%), Positives = 93/204 (45%), Gaps = 13/204 (6%)

Query: 48  QAYAIANGRRLVGRKIGLTNPKVQAQLGVDQPDF----GCLFADMAYGDNEVIPFERVLQ 103
           +AYAI +    V R++G   P V  ++G   PD       + AD  + D   +P      
Sbjct: 39  EAYAIQDA---VARRLG---PVVAWKVGARTPDTEPFRAPIHADTLFFDTTTLPAADYQV 92

Query: 104 PKIEAEIALILERDLPSASTTFA--DVIAATGWVVPALEVVGSRIEGWNIKFA-DTVADN 160
             +EAEIA    +DLP  +  ++  +V+ A   V PA E+V +R  G+  +     +AD 
Sbjct: 93  IGMEAEIAYKFAKDLPPRAEPYSREEVLDAVESVHPAFEIVDTRFAGFGSQDGLSHMADQ 152

Query: 161 ASSGCFVLGGPARRIDGLDLRGATMRMSKNGEVVSSGSGGECLGNPLNAAVWLARTMAEF 220
            + G  V+G        L+     + +  +GE  +    G   G P+   VW+A T A  
Sbjct: 153 FNHGALVVGPAIADWRSLEPLKERVALVVDGETKADTVAGNSAGEPVRLLVWMANTGAVS 212

Query: 221 GEPLKAGDIILTGALGPMVGVSAG 244
              LKAGD++ TG+    V V AG
Sbjct: 213 LGGLKAGDVVTTGSHVGTVMVPAG 236


Lambda     K      H
   0.317    0.136    0.395 

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: 201
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: 270
Length of database: 254
Length adjustment: 25
Effective length of query: 245
Effective length of database: 229
Effective search space:    56105
Effective search space used:    56105
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 (21.6 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