GapMind for catabolism of small carbon sources

 

Alignments for a candidate for padC in Dinoroseobacter shibae DFL-12

Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate 3607829 Dshi_1237 4Fe-4S ferredoxin iron-sulfur binding domain protein (RefSeq)

Query= uniprot:A0A2R4BLY8
         (215 letters)



>FitnessBrowser__Dino:3607829
          Length = 248

 Score =  117 bits (292), Expect = 2e-31
 Identities = 80/226 (35%), Positives = 98/226 (43%), Gaps = 44/226 (19%)

Query: 3   RYAMVADLRRCVGCQTCTAACKHTN---------------ATPPGVQWRWVLDVEAGEFP 47
           +  +V DL  CVGC  C  ACK  N               A P G     V   E     
Sbjct: 11  KLGLVIDLDTCVGCHACVVACKGWNDQAYGAPLSDQDPYGADPTGSFLNRVHSYEVTPAS 70

Query: 48  DVSR-TFVPVGCQHCDEPPCETVCPTTATKKRA-DGLVTIDYDLCIGCAYCSVACPYNAR 105
             ++    P  C HC++ PC TVCPT A+ KRA DG+V ++ D CIGC  C+ ACPY AR
Sbjct: 71  GPAQLVHFPKSCLHCEDAPCVTVCPTGASYKRAEDGIVLVNEDACIGCGLCAWACPYGAR 130

Query: 106 YKVNFAEPAYGDRLMANEKQRADPARVGVATKCTFCSDRIDYGVAHGLTPGVDPDATPAC 165
                                   A  GV  KCT C DRI Y  A       + D  PAC
Sbjct: 131 EM---------------------DAAAGVMKKCTLCVDRI-YNEAL-----PEEDRQPAC 163

Query: 166 ANACIANALTFGDIDDPNSKASRLLRENEHFRMHEELGTGPGFFYL 211
              C A A  FGD+ DP+S+ S+L+       +  E GT P   YL
Sbjct: 164 VRTCPAGARHFGDLGDPDSEVSQLVAARGGVDLMPEQGTKPVNKYL 209


Lambda     K      H
   0.323    0.137    0.461 

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: 279
Number of extensions: 26
Number of successful extensions: 7
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: 215
Length of database: 248
Length adjustment: 23
Effective length of query: 192
Effective length of database: 225
Effective search space:    43200
Effective search space used:    43200
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 (21.9 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