GapMind for catabolism of small carbon sources

 

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

Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate WP_003944701.1 C1M55_RS12340 enoyl-CoA hydratase

Query= reanno::psRCH2:GFF2391
         (364 letters)



>NCBI__GCF_002893965.1:WP_003944701.1
          Length = 259

 Score = 73.9 bits (180), Expect = 4e-18
 Identities = 55/186 (29%), Positives = 92/186 (49%), Gaps = 6/186 (3%)

Query: 8   VLAAVRNHVGHLTLNRPAGLNAVTLEMVRLLQQQLSAWAADPQIHAVVLRANGEKAFCAG 67
           V   V   +G + L RP  +NA+  ++   L     A   D  + AV++   GEK F AG
Sbjct: 5   VTLEVSEGIGTIRLARPP-MNALNRQVQDELAAAAHAATVDKAVKAVIVYG-GEKVFAAG 62

Query: 68  GDIRSLYDSFQRGDTEHETFFEEEYALDQYIHAYPKPLLALMDGFVLGGGMGLVQGASLR 127
            D++ + +    G    +     +  L   + + PKP +A + G+ LGGG+ +   A  R
Sbjct: 63  ADVKEMAE-MDYGQIR-DAIGGMQAGLGA-VASIPKPTVAAITGYALGGGLEVALSADRR 119

Query: 128 VVTERVRMGMPEVGIGYFPDVGGSYFLSRLPGEL-GTYMGVTGLQIRAADALHVGLADWC 186
           +V +  ++G+PE+ +G  P  GG+  L+RL G      +  TG  + A +AL +GL D  
Sbjct: 120 IVGDNAKLGVPEILLGIIPGGGGTQRLARLIGPAKAKDLVFTGRFVGADEALAIGLVDEV 179

Query: 187 VSHDQI 192
           V+ D +
Sbjct: 180 VAPDDV 185


Lambda     K      H
   0.321    0.136    0.412 

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: 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: 364
Length of database: 259
Length adjustment: 27
Effective length of query: 337
Effective length of database: 232
Effective search space:    78184
Effective search space used:    78184
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 (21.9 bits)
S2: 48 (23.1 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