GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Marinobacter adhaerens HP15

Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate GFF2840 HP15_2784 3-ketoacyl-(acyl-carrier-protein) reductase

Query= BRENDA::Q1J2J0
         (255 letters)



>FitnessBrowser__Marino:GFF2840
          Length = 247

 Score =  137 bits (344), Expect = 3e-37
 Identities = 94/247 (38%), Positives = 134/247 (54%), Gaps = 17/247 (6%)

Query: 16  LDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLN-PDVGEGAARELDGTFERLNVTDA 74
           L G+ ALVTG ++GIG  IA  LAQ GA V I   +    GE  A+E++ T  R     A
Sbjct: 4   LKGKVALVTGASRGIGRHIALQLAQRGADVAINYRSRQSEGEEVAKEIEATGVRALSFKA 63

Query: 75  DA-----VADLARRLPD----VDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCC 125
           D         L R++ +    +D+LVNNAGI ++   +   DDDW  VL  NL  V+  C
Sbjct: 64  DLSKMPEARSLVRQVQEQWGRIDILVNNAGITKDKSMKKLTDDDWNDVLDTNLGSVYATC 123

Query: 126 REFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRV 185
            E  + M+ +  G I++  S  G   N    QA Y ASK  +I  T++LA E A   + V
Sbjct: 124 SEVLKIMMDQKYGRIINITSFVGQAGNF--GQANYAASKGGIIAFTKTLALEMAKYNITV 181

Query: 186 NAVAPGYTATPLTRRGLETPE-WRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGH 244
           NA+APG+T T +     + PE  RE  +   P+GR  +P EIA AV++LA++   ++TG 
Sbjct: 182 NAIAPGFTETEML---AQVPENIREQIIARVPMGRFGKPEEIARAVVFLAAE-GDYITGQ 237

Query: 245 TLVVDGG 251
            + V+GG
Sbjct: 238 QINVNGG 244


Lambda     K      H
   0.319    0.134    0.408 

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: 162
Number of extensions: 12
Number of successful extensions: 4
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: 255
Length of database: 247
Length adjustment: 24
Effective length of query: 231
Effective length of database: 223
Effective search space:    51513
Effective search space used:    51513
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 (21.8 bits)
S2: 46 (22.3 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