GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bch in Dechlorosoma suillum PS

Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate Dsui_2041 Dsui_2041 enoyl-CoA hydratase/carnithine racemase

Query= BRENDA::Q9LKJ1
         (378 letters)



>FitnessBrowser__PS:Dsui_2041
          Length = 261

 Score = 82.0 bits (201), Expect = 2e-20
 Identities = 73/232 (31%), Positives = 107/232 (46%), Gaps = 9/232 (3%)

Query: 5   MASQSQVLVEEKSSVRILTLNRPKQLNALSFHMISRLLQLFLAFEEDPSVKLVILKGHGR 64
           M+ ++ VL ++K  +  LTLNRP   NALS  MI+ L   F     DPS+ +VIL G+G 
Sbjct: 1   MSEEALVLRQDKDGIARLTLNRPAARNALSRPMIAALQAEFDRIAADPSIGVVILAGNGP 60

Query: 65  AFCAGGDVAAVVRDINQGNWRLGANYFSSEYMLNYVMATYSKAQVSILNGIVMGGGAGVS 124
           AFCAG D+   +R  + G  R   + F +   L   + +  +  ++ ++GI    GA + 
Sbjct: 61  AFCAGHDLKE-MRGADYGE-RYAEDLFEACARLMQRIVSLPQPVIARVHGIATAAGAQLV 118

Query: 125 VHGRFRIATENTVFAMPETALGLF---PDVGASYFLSRLPGFFGEYVGLTGARLDGAEML 181
                 IAT++  FA P   +GLF   P V  S  +S         + LTG  +D    L
Sbjct: 119 ASADLAIATDDARFATPGVNIGLFCSTPMVALSRNISHKHAL---QMLLTGDLIDAPTAL 175

Query: 182 ACGLATHFVPSTRL-TALEADLCRINSNDPTFASTILDAYTQHPRLKQQSAY 232
             GL    V   +L  A+EA   +I S      +    AY +   L    AY
Sbjct: 176 RFGLINEHVSGEQLDVAVEALAVKIASKSRHTLAVGKAAYYRQAELPLDEAY 227


Lambda     K      H
   0.321    0.136    0.396 

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: 192
Number of extensions: 7
Number of successful extensions: 2
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: 378
Length of database: 261
Length adjustment: 27
Effective length of query: 351
Effective length of database: 234
Effective search space:    82134
Effective search space used:    82134
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 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