GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dddA in Phaeobacter inhibens BS107

Align 3-hydroxypropanonate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate GFF1712 PGA1_c17360 3-hydroxyisobutyrate dehydrogenase MmsB

Query= metacyc::MONOMER-18957
         (354 letters)



>FitnessBrowser__Phaeo:GFF1712
          Length = 291

 Score =  127 bits (319), Expect = 4e-34
 Identities = 96/318 (30%), Positives = 147/318 (46%), Gaps = 41/318 (12%)

Query: 18  NYGFIGLGLMGQHMARHVYNQLEPSDKLYVYDVDPKHTTQFLTEVTSQTPQNAPLLTPLN 77
           N GFIGLG MG  MA ++           + DV  +  T   +                 
Sbjct: 2   NIGFIGLGNMGGPMAANLAKAGHDVTGFDMADVSIEGVTMAAS----------------- 44

Query: 78  SLKDFTTEVDSQLDFIVTMVPEGKHVKSVVSELVGHYKSTGNYDPSIKTTFLDSSTIDIP 137
                  E  +  + ++TM+P G+ +++V  +++           S   T +D ST+D+ 
Sbjct: 45  -----AAEAATDAEVVITMLPNGQILRAVADDVIPAM--------SAGATLVDCSTVDVD 91

Query: 138 TSRDVHQLVKSSIPEFDFIDTPVSGGVAGARKGTLSFML--SRETHDDIDPSLTALLSKM 195
           ++R V     S+     F+D PVSGG+ GA  GTL+FM   S       +P    L   M
Sbjct: 92  SARAVADQAGSA--NLMFVDAPVSGGIGGASGGTLTFMAGGSAAAFAAAEP----LFDIM 145

Query: 196 GINIFPCGATHGTGLAAKLANNYLLAITNIAAADSFQLAESFGLNLQNYAKLVAVSTGKS 255
           G     CG   G G AAK+ NN +L IT I   ++F LA+  GL+ Q    +V+ S+G S
Sbjct: 146 GQKAVHCGEA-GAGQAAKICNNMILGITMIGTCEAFALADKLGLDRQKMFDVVSTSSGYS 204

Query: 256 WASVDNCPIPGVYPDNNLPSDVNYEGGFITKLTRKDVVLATESAKFNNRFLMLGDIGRHW 315
           W+    CP PGV P +  P+D +Y+ GF  +L  KD+ LA ++A   +    +G + +  
Sbjct: 205 WSMNAYCPAPGVGPQS--PADNDYQPGFAAELMLKDLRLAQQAAHSADADTPMGALAQAL 262

Query: 316 YDKACEREDIANRDLSVL 333
           Y    E E  A +D S +
Sbjct: 263 YSMFVEDEGGAGKDFSAM 280


Lambda     K      H
   0.317    0.134    0.392 

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: 210
Number of extensions: 10
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 354
Length of database: 291
Length adjustment: 28
Effective length of query: 326
Effective length of database: 263
Effective search space:    85738
Effective search space used:    85738
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 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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