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 GFF3989 HP15_3929 acyl-CoA dehydrogenase domain protein

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



>FitnessBrowser__Marino:GFF3989
          Length = 398

 Score =  448 bits (1152), Expect = e-130
 Identities = 219/403 (54%), Positives = 291/403 (72%), Gaps = 12/403 (2%)

Query: 1   MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60
           M+LN++ EE+AFRDEVR F    +P     K+   R  +KE+   W +IL+++GW  THW
Sbjct: 1   MNLNYTTEELAFRDEVRAFLDKKLPGDIAAKVKGFRRLSKEDHQRWQKILSEQGWYATHW 60

Query: 61  PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120
           P+EYGG  WS VQ +I++EE     AP+ + FGV+MV PVI  FG+EEQK+R+LPRI + 
Sbjct: 61  PEEYGGVNWSPVQKHIWDEESSRYGAPRSVPFGVNMVAPVIIKFGTEEQKQRYLPRILSG 120

Query: 121 DDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAK 180
           +DWWCQG+SEPG+GSDLASLKT+A + GD +I+NGQKTWTTL QHA+ IFCL RT+   K
Sbjct: 121 EDWWCQGYSEPGAGSDLASLKTRAVRDGDHYIVNGQKTWTTLGQHANMIFCLVRTNTEVK 180

Query: 181 KQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFL 240
            QEGISF+L+DM T GITVRPI T+DG HEVNEVFF+DV+VP ENLVG+E+KGW YAK+L
Sbjct: 181 AQEGISFLLIDMDTPGITVRPIITLDGEHEVNEVFFEDVKVPAENLVGEEDKGWTYAKYL 240

Query: 241 LGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALELTQL 300
           L  ERTG+A +G+SK  ++ +K+LA +    G+P+IED  F  ++A VEI+L A  ++ L
Sbjct: 241 LTYERTGLAGIGISKAALQHLKELATRRVKNGRPLIEDASFGQRIAQVEIDLMAAAISNL 300

Query: 301 RVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPY-------DVHGDD 353
           R++A     G G P   SS+LK++G+EI+Q   +L    IGP+A P+       D  GD 
Sbjct: 301 RIIA--SVEGGGMPGAESSMLKVRGTEIRQTINDLARRAIGPYAIPFVEEELDLDYDGDF 358

Query: 354 DSNETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396
            S+E     A +AP YFNNRK+SI+GGSNEIQ+NI+ K +LGL
Sbjct: 359 LSDEN---AAPVAPQYFNNRKLSIFGGSNEIQKNIVSKMILGL 398


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: 494
Number of extensions: 18
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: 398
Length adjustment: 31
Effective length of query: 365
Effective length of database: 367
Effective search space:   133955
Effective search space used:   133955
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