GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Marinobacter adhaerens HP15

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate GFF53 HP15_53 acyl-CoA dehydrogenase domain protein

Query= metacyc::MONOMER-20676
         (396 letters)



>FitnessBrowser__Marino:GFF53
          Length = 383

 Score =  176 bits (447), Expect = 8e-49
 Identities = 128/393 (32%), Positives = 196/393 (49%), Gaps = 26/393 (6%)

Query: 7   KEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHWPKEYGG 66
           +E    R EV+ F K  +   T   L +  H+      E+ R L  KGW     P +YGG
Sbjct: 13  QEAELLRSEVQSFLKSEL---TDYPLSDRAHSWMGFDAEFSRKLGAKGWLGMSLPIQYGG 69

Query: 67  TGWSSVQHYIFNEELQAAPAPQPLAFGVS-MVGPVIYTFGSEEQKKRFLPRIANVDDWWC 125
              S    Y+  EEL AA AP    +      GP+I  FG+ EQK++FLP I   + ++C
Sbjct: 70  AEASPFARYVVIEELLAAGAPVSAHWIADRQSGPLIQRFGTAEQKEKFLPSICKGESFFC 129

Query: 126 QGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAK--KQE 183
            G SEP SGSDLAS+KT A++  + W++NGQK WTT A  + ++  L RT    +  +  
Sbjct: 130 IGMSEPDSGSDLASIKTNAKRTDNGWVLNGQKVWTTNAHLSHYMIALVRTGDREETGRHG 189

Query: 184 GISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFLLGN 243
           G+S  ++D+   G+TVR I  + GG   NEVFFD+V +  + L+G+E  GW      L  
Sbjct: 190 GMSQFIIDLSLPGVTVRAIPDLTGGEHFNEVFFDNVALEKDALIGEEGAGWQQVTAELAF 249

Query: 244 ERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALELTQLRVV 303
           ER+G  R   S   +      AA    G  P     +   ++ A  + L+ + L+  + +
Sbjct: 250 ERSGPERFLSSIALV-----YAALDVIGTNPDALQSRDIGRITARLLTLRDMSLSVTQQL 304

Query: 304 ADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHGDDDSNETMDWTA 363
           +D G++    P  A+S +K  G+  +Q   E+L  +I        + G  + +  + +  
Sbjct: 305 SD-GEN----PAWAASCVKDLGNAFEQEIPEILQLLI---EQQPQIDGGSEYSRVLAYLT 356

Query: 364 QIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396
           Q+AP +      S+ GG+ EI R II +  LGL
Sbjct: 357 QMAPSF------SLRGGTREILRGIIARG-LGL 382


Lambda     K      H
   0.317    0.135    0.411 

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: 362
Number of extensions: 17
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: 396
Length of database: 383
Length adjustment: 30
Effective length of query: 366
Effective length of database: 353
Effective search space:   129198
Effective search space used:   129198
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: 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