GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Flavobacterium sp. LM5

Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_024981780.1 BXU11_RS13235 3-oxoacyl-[acyl-carrier-protein] reductase

Query= uniprot:Q8EGC1
         (252 letters)



>NCBI__GCF_002017945.1:WP_024981780.1
          Length = 248

 Score =  132 bits (332), Expect = 7e-36
 Identities = 89/255 (34%), Positives = 136/255 (53%), Gaps = 19/255 (7%)

Query: 3   LKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACA---DLGS-STEVQGY 58
           L+ KV +ITG + G+G  +A  FA+ GA +A        +E A A   +L +   + +GY
Sbjct: 4   LEGKVAIITGASRGIGKGIAEVFAKHGANIAF--TYSSSVESALALENELNTMGIKAKGY 61

Query: 59  ALDITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVI 118
             +  D  +       +L DFG +++L+NNAGI +D +++         RMS   F  VI
Sbjct: 62  QSNAADFNEAQTFVDAVLADFGSVDILINNAGITKDNLMM---------RMSEADFDQVI 112

Query: 119 NVNLTGTFLCGREAAAAMIESGQAGVIVNISSLAKA-GNVGQSNYAASKAGVAAMSVGWA 177
           +VNL   F   +      ++  +AG I+N+SS+    GN GQ+NYAASKAGV   S   A
Sbjct: 113 DVNLKSVFNMTKAIQKTFLKQ-RAGSIINMSSVVGVKGNAGQTNYAASKAGVIGFSKSVA 171

Query: 178 KELARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIE-- 235
            EL   NIR   +APG I TEMTA +  + ++   + +P+ R G  +++A+   F     
Sbjct: 172 LELGSRNIRCNVIAPGFIETEMTAKLSDDVVKGWREGIPLKRGGSTDDVANACLFFASDM 231

Query: 236 NDYVNGRVFEVDGGI 250
           + YV G+V  V GG+
Sbjct: 232 SAYVTGQVLNVCGGM 246


Lambda     K      H
   0.317    0.134    0.369 

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: 166
Number of extensions: 12
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: 252
Length of database: 248
Length adjustment: 24
Effective length of query: 228
Effective length of database: 224
Effective search space:    51072
Effective search space used:    51072
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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