GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpD in Rhodococcus qingshengii djl-6-2

Align 2-oxopent-4-enoate hydratase (EC 4.2.1.80) (characterized)
to candidate WP_102999320.1 C1M55_RS04075 2-keto-4-pentenoate hydratase

Query= metacyc::MONOMER-14738
         (279 letters)



>NCBI__GCF_002893965.1:WP_102999320.1
          Length = 261

 Score =  208 bits (529), Expect = 1e-58
 Identities = 111/249 (44%), Positives = 149/249 (59%)

Query: 29  DELYQSLLDRQPVAPLTDREADITIEDAYQIQLRMIQRRLDAGERVVGKKIGVTSKVVMD 88
           D L  +  DR P++PL     DI + DAY+IQL  I+RR+  G +VVG K+G++S  +  
Sbjct: 12  DHLDSAERDRAPISPLIATYPDIDVVDAYEIQLINIRRRVAGGAKVVGHKVGLSSLAMQQ 71

Query: 89  MLKVNQPDFGHLLSGMVYNEGQPIPVSSMIAPKAEAEVAFILARDLEGPGVTAADVLRAT 148
           M+ V++PD+GHLL+ M   E +P+  S    P+ E EVAFIL  DL G G T  DV+ AT
Sbjct: 72  MMGVDEPDYGHLLAEMEEFENRPVDTSRFCFPRVEVEVAFILGADLPGAGCTEQDVIDAT 131

Query: 149 DCVMPCFEIVDSRIKDWKIKIQDTVADNASCGVLTLGGLRKSPRDLDLALAGMVLEKNGE 208
               P  E++DSRIKDWKI + DT+ADNAS     LG  R  P D+D+     VL  NGE
Sbjct: 132 VAYAPSIELIDSRIKDWKIGLSDTIADNASSAGFILGKERVRPSDIDIKAIDAVLTCNGE 191

Query: 209 IISTSCGASVQGSPVNAVAWLANTLGRLGIGLKAGDIILSGSQSPLVPVVAGDSLYCSVG 268
            I+     +V G+PV AVAWLA  +   G+ LKAGDI+L GS +  +    GD+      
Sbjct: 192 RIAEGRSDAVLGNPVTAVAWLAQKVDTFGVWLKAGDIVLPGSCTRAIDAHPGDNFRAEFS 251

Query: 269 GLGGTSVRF 277
           GLG  S++F
Sbjct: 252 GLGSVSLQF 260


Lambda     K      H
   0.318    0.136    0.390 

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: 194
Number of extensions: 8
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: 279
Length of database: 261
Length adjustment: 25
Effective length of query: 254
Effective length of database: 236
Effective search space:    59944
Effective search space used:    59944
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 24 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