GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Dechlorosoma suillum PS

Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate Dsui_1378 Dsui_1378 enoyl-CoA hydratase/carnithine racemase

Query= BRENDA::Q1D5Y4
         (258 letters)



>FitnessBrowser__PS:Dsui_1378
          Length = 258

 Score =  165 bits (418), Expect = 8e-46
 Identities = 95/252 (37%), Positives = 142/252 (56%), Gaps = 2/252 (0%)

Query: 7   DARGPIEIWTIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGADL 66
           +A+G + + T++     NA+   ++ ELG+ +T   +  ++  +VITG+ DKAF AGAD+
Sbjct: 9   EAKGRVGLITLNRPKALNALCDPLVDELGDALTEFEADENIGCIVITGS-DKAFAAGADI 67

Query: 67  KERATMAEDEVRAFLDGLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPAA 126
                 +  +     D + R +  ++      IAA+ G ALGGG ELA++CD  +AA +A
Sbjct: 68  SMMKDFSYMDAYKG-DYITRNWEKVKTCRKPVIAAVAGYALGGGCELAMSCDFIIAADSA 126

Query: 127 ELGLTEVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGHL 186
           + G  EVKLGI+PG GGTQRL R VG  +A DL L+AR ++A EA   GL +R+ P   L
Sbjct: 127 QFGQPEVKLGILPGAGGTQRLPRAVGKAKAMDLCLSARMMDATEAERAGLVSRIVPADKL 186

Query: 187 LAVAYGLAESVVENAPIAVATAKHAIDEGTGLELDDALALELRKYEEILKTEDRLEGLRA 246
           L  A G AE +   +   V   K  ++      L++ L  E R++      ED+ EG+ A
Sbjct: 187 LEEALGAAEKIASYSLPVVMMIKENVNRAFESSLNEGLLFERRQFHAAFALEDQKEGMAA 246

Query: 247 FAEKRAPVYKGR 258
           F EKR P +K R
Sbjct: 247 FVEKRKPAFKHR 258


Lambda     K      H
   0.319    0.136    0.380 

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: 145
Number of extensions: 9
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: 258
Length of database: 258
Length adjustment: 24
Effective length of query: 234
Effective length of database: 234
Effective search space:    54756
Effective search space used:    54756
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 (21.7 bits)
S2: 47 (22.7 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