GapMind for catabolism of small carbon sources

 

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

Align 4-oxalocrotonate decarboxylase; 4-OD; EC 4.1.1.77 (uncharacterized)
to candidate WP_102999320.1 C1M55_RS04075 2-keto-4-pentenoate hydratase

Query= curated2:P49156
         (264 letters)



>NCBI__GCF_002893965.1:WP_102999320.1
          Length = 261

 Score =  181 bits (458), Expect = 2e-50
 Identities = 99/251 (39%), Positives = 145/251 (57%)

Query: 13  LAEHIENAELDVHDIPKVTNDYPDMTFADAYDVQWEIRRRKEARGNKVVGLKMGLTSWAK 72
           LA+H+++AE D   I  +   YPD+   DAY++Q    RR+ A G KVVG K+GL+S A 
Sbjct: 10  LADHLDSAERDRAPISPLIATYPDIDVVDAYEIQLINIRRRVAGGAKVVGHKVGLSSLAM 69

Query: 73  MAQMGVETPIYGFLVDYFSVPDGGVVDTSKLIHPKIEAEISFVTKAPLHGPGCHIGQVLA 132
              MGV+ P YG L+      +   VDTS+   P++E E++F+  A L G GC    V+ 
Sbjct: 70  QQMMGVDEPDYGHLLAEMEEFENRPVDTSRFCFPRVEVEVAFILGADLPGAGCTEQDVID 129

Query: 133 ATDFVIPTVEVIDSRYENFKFDLISVVADNASSTRFITGGQMANVADLDLRTLGVVMEKN 192
           AT    P++E+IDSR +++K  L   +ADNASS  FI G +    +D+D++ +  V+  N
Sbjct: 130 ATVAYAPSIELIDSRIKDWKIGLSDTIADNASSAGFILGKERVRPSDIDIKAIDAVLTCN 189

Query: 193 GEVVELGAGAAVLGHPASSVAMLANLLAERGEHIPAGSFIMTGGITAAVPVAPGDNITVR 252
           GE +  G   AVLG+P ++VA LA  +   G  + AG  ++ G  T A+   PGDN    
Sbjct: 190 GERIAEGRSDAVLGNPVTAVAWLAQKVDTFGVWLKAGDIVLPGSCTRAIDAHPGDNFRAE 249

Query: 253 YQGLCSVSARF 263
           + GL SVS +F
Sbjct: 250 FSGLGSVSLQF 260


Lambda     K      H
   0.320    0.136    0.396 

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: 195
Number of extensions: 9
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: 264
Length of database: 261
Length adjustment: 25
Effective length of query: 239
Effective length of database: 236
Effective search space:    56404
Effective search space used:    56404
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 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