GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garL in Herbaspirillum seropedicae SmR1

Align 5-keto-4-deoxy-D-glucarate aldolase; KDGluc aldolase; KDGlucA; 2-dehydro-3-deoxy-D-glucarate aldolase; 2-keto-3-deoxy-D-glucarate aldolase; 5-dehydro-4-deoxy-D-glucarate aldolase; Alpha-keto-beta-deoxy-D-glucarate aldolase; EC 4.1.2.20 (characterized)
to candidate HSERO_RS01600 HSERO_RS01600 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase

Query= SwissProt::P23522
         (256 letters)



>FitnessBrowser__HerbieS:HSERO_RS01600
          Length = 250

 Score =  132 bits (332), Expect = 7e-36
 Identities = 80/235 (34%), Positives = 123/235 (52%), Gaps = 5/235 (2%)

Query: 8   NKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALKG 67
           N+ +   A +Q+ +  W ++ N +  EV+  +G+D + +D +H P  I   +P L A+  
Sbjct: 4   NRLRTLFAQQQLALSGWVSMGNALLAEVIAHSGYDAVTVDLQHGPFSIDAALPMLQAISS 63

Query: 68  SASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVSH 127
           + + P+VR   N    I +LLD G Y  + P + T  +AE  V +  Y P G R    + 
Sbjct: 64  TPAVPLVRCSENSLGEINKLLDAGAYGVICPLINTAADAERFVRACHYSPRGGRSYGPA- 122

Query: 128 RANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGHL 187
           R  ++G  ADYF  +N  +  L  IE+++G  N +AI  T  +DGIF+GPSDLA  LG L
Sbjct: 123 RGFLYGG-ADYFTHANATLLTLAMIETREGYANAEAILQTPDLDGIFIGPSDLAIELG-L 180

Query: 188 GNASHPDVQ--KAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDL 240
              ++ DV+  +AI H+   A   GK  GI A     A+R    G   V  G+D+
Sbjct: 181 APDAYDDVRLNEAIDHLLALARKLGKYVGIFAGTMEMAQRMKGIGMDLVVPGTDI 235


Lambda     K      H
   0.318    0.134    0.392 

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: 136
Number of extensions: 6
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: 256
Length of database: 250
Length adjustment: 24
Effective length of query: 232
Effective length of database: 226
Effective search space:    52432
Effective search space used:    52432
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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