GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bch in Rhodobacter viridis JA737

Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate WP_110804536.1 C8J30_RS04555 enoyl-CoA hydratase

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



>NCBI__GCF_003217355.1:WP_110804536.1
          Length = 258

 Score = 79.7 bits (195), Expect = 8e-20
 Identities = 57/177 (32%), Positives = 89/177 (50%), Gaps = 8/177 (4%)

Query: 8   VLAAVRNHVGHLTLNRPAGLNAVTLEMVRLLQQQLSAWAADPQIHAVVLRANGEKAFCAG 67
           ++  + + V  + LNRP  LNA+  +++  L + L    ADP +   VL  + +KAF AG
Sbjct: 6   LIVEIEDGVALIRLNRPEALNALNSQLLGELAEALKTLDADPAVRCFVLTGS-DKAFAAG 64

Query: 68  GDIRSLYD-SFQRGDTEHETFFEEEYALDQYIHAYPKPLLALMDGFVLGGGMGLVQGASL 126
            DI+ + D SF   D   + FF  E      I    KP++A + G+ LGGG  L      
Sbjct: 65  ADIKEMADKSFT--DMFLQDFFGTE---GDAILRTRKPIIAAVAGYALGGGCELAMMCDF 119

Query: 127 RVVTERVRMGMPEVGIGYFPDVGGSYFLSRLPGELGTY-MGVTGLQIRAADALHVGL 182
            +  E  + G PE+ +G    +GG+  L+R  G+  +  M +TG  + AA+A   GL
Sbjct: 120 ILCAENAKFGQPEINLGVVAGIGGTQRLTRFVGKSKSMEMHLTGRFMDAAEAERSGL 176


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: 197
Number of extensions: 9
Number of successful extensions: 3
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: 258
Length adjustment: 27
Effective length of query: 337
Effective length of database: 231
Effective search space:    77847
Effective search space used:    77847
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