GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fuconolactonase in Ruegeria conchae TW15

Align Metal-dependent hydrolase of the TIM-barrel fold protein (characterized, see rationale)
to candidate WP_010442380.1 G7G_RS0115640 amidohydrolase family protein

Query= uniprot:D8J114
         (289 letters)



>NCBI__GCF_000192475.1:WP_010442380.1
          Length = 303

 Score = 99.4 bits (246), Expect = 9e-26
 Identities = 91/303 (30%), Positives = 137/303 (45%), Gaps = 36/303 (11%)

Query: 6   IDAHQHFWFYQPQAYPWIGA-GMELLACDRTP-------GQLQPLLDAEGLGQSIAVQAR 57
           IDAH H W  +   YPW+ A G+E    D TP        + Q      G+G SI +Q  
Sbjct: 5   IDAHHHLWDLEAVYYPWLMARGVERFFGDPTPIQRNYQLSEFQSEAAPCGIGASIHIQVG 64

Query: 58  A--GREETGFLLELARGNRR--IAGVVGWEDLASPHLAANVERW-------GRDKLVGFR 106
           A  G +E  ++  +A  N    +A VV + DL S  L+A ++ +       G  ++VG  
Sbjct: 65  AENGLDEARWVQSVADANSDWPMAQVV-YCDLTSTELSAQLDTFQTLPTVRGVRQIVGRA 123

Query: 107 HQLQDEADVGGCVDAPAFNAGVAWLQRQGMVYDVLVYARQMAEVQAFCARHDRHWLVLDH 166
                +      +D P F  G+       + +D+ +    M +     A      + L H
Sbjct: 124 PGEDAQTGTNALLDDPQFLIGLKEAGICNLSFDLQLVPELMKKTARVLALAPDIRVALCH 183

Query: 167 LGKPALTEFGRGDTAFEGWQRQLRALAALPHVACKLSGL-VTEADWQRGLRQKDFDNISL 225
            G P      R     + W + LRAL+ LP+V+CKLSGL + + +W         D+I  
Sbjct: 184 AGSP----HDRSPAGLKEWAQNLRALSNLPNVSCKLSGLGMFDHNWT-------LDSIRP 232

Query: 226 CLDTALEAFGPQRLMFGSDWPVCLLAASYAKVAGVVREWAATRLSAAEQELLWGATAARC 285
            +D  LE FGP+R+MFGS++PV  L   YA +A V R+     + A     ++  TA R 
Sbjct: 233 IVDECLEQFGPKRVMFGSNFPVDKLYGDYATLAEVYRD----LVPAESHSAVFSETAIRF 288

Query: 286 YGL 288
           Y L
Sbjct: 289 YDL 291


Lambda     K      H
   0.324    0.137    0.450 

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: 257
Number of extensions: 18
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: 289
Length of database: 303
Length adjustment: 26
Effective length of query: 263
Effective length of database: 277
Effective search space:    72851
Effective search space used:    72851
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 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