GapMind for catabolism of small carbon sources

 

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

Align 3-oxoadipate CoA-transferase (EC 2.8.3.6) (characterized)
to candidate WP_050654880.1 C1M55_RS10590 3-oxoadipate--succinyl-CoA transferase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4591
         (259 letters)



>NCBI__GCF_002893965.1:WP_050654880.1
          Length = 261

 Score =  186 bits (473), Expect = 3e-52
 Identities = 101/241 (41%), Positives = 143/241 (59%), Gaps = 1/241 (0%)

Query: 4   TTNEMMTVAAARRLKNGSVCFVGIGLPSKAANLARLTSSPDVVLIYESGPIGAKPSVLPL 63
           T+ E +   AAR L      F G+GLP+ A +LAR TS+PDV LIYESG  GA PS +  
Sbjct: 11  TSTETIVAVAARELAGKRRVFAGVGLPTLAVDLARHTSNPDVELIYESGVCGAHPSAMAE 70

Query: 64  SIGDGELAETADTVVPTGEIFRYWLQGGRIDVGFLGAAQVDRFGNINTTVVGDYHAPKVR 123
            I D  +   A++V+    +F Y LQGG +DVGFLGAAQ+DR G++NT+ +GD+  P VR
Sbjct: 71  GIADSVVVSGAESVLSMAALFGYVLQGGNVDVGFLGAAQIDRTGSLNTSFIGDWKNPTVR 130

Query: 124 LPGAGGAPEIAGSAKSVLIILKQSS-RSFVDKLDFITSVGHGEGGDSRKRLGLPGAGPVG 182
           LPGAGGA EI  +A  + +++++    SF   LDF TS        S K +   GAG   
Sbjct: 131 LPGAGGAVEIIANAAEIFVVMRRHDLSSFPAALDFCTSPSPARAHASGKGIMPAGAGVTK 190

Query: 183 IITDLCIMEPEAGTHEFVVTALHPGVTREQVVDATGWAIRFADQVEQTAEPTEVELTALR 242
           + T+L ++  +    E  +T++H G++  QV +ATGW +  AD V  T  P+  E+  LR
Sbjct: 191 VFTNLGVLTHQGPGGELELTSVHEGISVHQVREATGWDLAVADHVTVTTPPSGTEIDLLR 250

Query: 243 D 243
           +
Sbjct: 251 N 251


Lambda     K      H
   0.316    0.135    0.393 

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: 207
Number of extensions: 7
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: 259
Length of database: 261
Length adjustment: 24
Effective length of query: 235
Effective length of database: 237
Effective search space:    55695
Effective search space used:    55695
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 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