GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Collimonas arenae Ter10

Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate WP_061533914.1 CAter10_RS14240 3-hydroxybutyrate dehydrogenase

Query= SwissProt::Q9NKW1
         (441 letters)



>NCBI__GCF_001584165.1:WP_061533914.1
          Length = 260

 Score =  105 bits (261), Expect = 2e-27
 Identities = 72/212 (33%), Positives = 107/212 (50%), Gaps = 14/212 (6%)

Query: 3   LNFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKA 62
           ++ KDKV ++TG+  GIGK  A+E+A+ GAKVV+ DL            AA     EI  
Sbjct: 1   MSLKDKVALITGSASGIGKEIAIEYARAGAKVVIADL---------QLDAATATANEITQ 51

Query: 63  AGGTAVANYDSVEDG---EKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYR 119
           +GG A+A   +V D    +K +   + ++G +D+LI+NAGI         T  +W  +  
Sbjct: 52  SGGIAMAVAMNVTDETQVDKGIADTVAAYGSIDVLISNAGIQIIAPIVDSTLDNWKKMLA 111

Query: 120 VHAKGAYKLSRAAWNHMREK-NFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQ 178
           +H  GAY  +RAA   M +K N G II   S      +  +A Y + K  L+GL+  +A+
Sbjct: 112 IHLDGAYLTTRAAMREMIKKGNGGSIIYMGSVHSHEASPLKAPYVTAKHGLIGLAKVVAK 171

Query: 179 EGKSKNIHCNTIAP-IAASRLTESVMPPEILE 209
           EG    I  N I P    + L E  +P +  E
Sbjct: 172 EGAKNKIRANVICPGFVRTPLVEKQIPEQAKE 203


Lambda     K      H
   0.313    0.131    0.371 

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: 238
Number of extensions: 13
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: 441
Length of database: 260
Length adjustment: 28
Effective length of query: 413
Effective length of database: 232
Effective search space:    95816
Effective search space used:    95816
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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