GapMind for catabolism of small carbon sources

 

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

Align 4-oxalocrotonate decarboxylase; EC 4.1.1.77 (characterized)
to candidate WP_076948744.1 C1M55_RS02650 4-oxalocrotonate decarboxylase

Query= SwissProt::Q9KWS3
         (256 letters)



>NCBI__GCF_002893965.1:WP_076948744.1
          Length = 257

 Score =  208 bits (530), Expect = 8e-59
 Identities = 112/247 (45%), Positives = 165/247 (66%), Gaps = 3/247 (1%)

Query: 3   ISRIAQRLDEAAVSGKATPQLTGDDAVTVREAAEIQRLLIAHRIERGARQVGLKMGFTSR 62
           +S +A+RLD+AA +   TP L  +  + + +A  IQ  L+  R  RG   VG+K+GFTS+
Sbjct: 8   VSALARRLDDAAQTRTDTPSLADEHTIDIDQAYRIQNELLERRTSRGESIVGIKLGFTSK 67

Query: 63  AKMAQMGVSDLIWGRLTSDMWVEEGGEIDLAHYVHPRVEPEICYLLGKRLEGNVTPLEAL 122
           AKMAQMGVS +I G+LT  M V  GGE+DL  ++HP++EPE+ Y L K ++ +   ++  
Sbjct: 68  AKMAQMGVSGVIVGQLTDAMCVSNGGEVDLRTFIHPKIEPEVAYRLSKDVDLDDPNVDIE 127

Query: 123 AAVEAVAPAMEIIDSRYRDFKFSLPDVIADNASSSGFVVGAWHKPETDVSNLGMVMSFDG 182
             V+A+APAMEIIDSRYRDF+F+  DV+ADN S++G+V+G W  P  +V +  + M   G
Sbjct: 128 TCVDALAPAMEIIDSRYRDFRFTYTDVVADNTSAAGYVIGRW-LPLQNVEDRSVRMEVGG 186

Query: 183 RAVELGTSAAILGSPIRALVAAARLAAQQGEALEAGSLILAGAATAAVALRPGISVRCEV 242
             V +G+++AILG P RAL     +A ++   L AG +ILAGAATAAV L  G++ +C +
Sbjct: 187 ETV-VGSTSAILGDPARALHELLDIARRRRIPLRAGQVILAGAATAAVRLDEGVA-QCTI 244

Query: 243 QNLGSLS 249
             LG+++
Sbjct: 245 DGLGTVT 251


Lambda     K      H
   0.318    0.132    0.372 

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: 156
Number of extensions: 6
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: 256
Length of database: 257
Length adjustment: 24
Effective length of query: 232
Effective length of database: 233
Effective search space:    54056
Effective search space used:    54056
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