GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimC in Marinobacter adhaerens HP15

Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate GFF3988 HP15_3928 acyl-CoA dehydrogenase domain protein

Query= metacyc::MONOMER-20677
         (380 letters)



>FitnessBrowser__Marino:GFF3988
          Length = 378

 Score =  352 bits (902), Expect = e-101
 Identities = 183/375 (48%), Positives = 239/375 (63%)

Query: 1   MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60
           MDF L+EEQ++L+++V  L++G Y F+ R +Y++   G+S   W +  E GL  +PF EE
Sbjct: 1   MDFRLNEEQQMLQDTVARLVRGEYSFEKRLEYSESGLGFSADFWKQLGELGLTAVPFPEE 60

Query: 61  DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSKT 120
            GGFG   VE   VM  LG  L +EPYL +VV+GGG + +AG++AQ+   L GI  G   
Sbjct: 61  LGGFGGTGVEVQSVMTELGRGLCVEPYLQSVVLGGGLISQAGNSAQQEQWLGGIASGEIR 120

Query: 121 FAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRT 180
            A    E  S ++L DV T A+KS DG+V++G K VV+ G  AD L+V+ART G  RD  
Sbjct: 121 AAVGLQEPQSFYNLNDVDTRAEKSDDGYVLNGRKAVVIGGHCADVLVVSARTSGDSRDAE 180

Query: 181 GVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDA 240
           G+ +FL+PADA+G+ R+ YPT DG    D+    VQ+G DA +GD   A E+IE     A
Sbjct: 181 GISLFLIPADAEGVERRTYPTIDGSKGCDLFLNNVQLGTDALLGDEGKAAEVIEYQSGRA 240

Query: 241 RTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFA 300
            +ALC EAVG M+ +   T+EY+K RKQFGVPIG FQVLQHR  DM    EQARSMA+ A
Sbjct: 241 ISALCGEAVGAMEVACDLTLEYLKQRKQFGVPIGKFQVLQHRMVDMMSELEQARSMAILA 300

Query: 301 TMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMIE 360
              A+   + ER   +AAAK  IG+SG+F+ +Q IQ HGGIGMT E    HY KRL MI 
Sbjct: 301 ASVADEPQSDERRRILAAAKNVIGRSGQFISEQGIQSHGGIGMTWEYNFAHYAKRLVMIN 360

Query: 361 QTFGDTDHHLARVSA 375
              GD D HL R +A
Sbjct: 361 HQLGDDDFHLERYAA 375


Lambda     K      H
   0.318    0.135    0.388 

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: 400
Number of extensions: 18
Number of successful extensions: 1
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: 380
Length of database: 378
Length adjustment: 30
Effective length of query: 350
Effective length of database: 348
Effective search space:   121800
Effective search space used:   121800
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 (21.7 bits)
S2: 50 (23.9 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