GapMind for catabolism of small carbon sources

 

Alignments for a candidate for padC in Magnetospirillum magneticum AMB-1

Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate WP_011383654.1 AMB_RS06305 4Fe-4S dicluster domain-containing protein

Query= uniprot:A0A2R4BLY8
         (215 letters)



>NCBI__GCF_000009985.1:WP_011383654.1
          Length = 217

 Score =  325 bits (832), Expect = 5e-94
 Identities = 145/213 (68%), Positives = 170/213 (79%)

Query: 1   MTRYAMVADLRRCVGCQTCTAACKHTNATPPGVQWRWVLDVEAGEFPDVSRTFVPVGCQH 60
           MT++A+VADL RCVGCQTCT AC+H NATPPGVQ+R VLD+E G FPDV R FVPVGC H
Sbjct: 1   MTKWAIVADLGRCVGCQTCTTACRHANATPPGVQYRKVLDMEVGTFPDVRRVFVPVGCMH 60

Query: 61  CDEPPCETVCPTTATKKRADGLVTIDYDLCIGCAYCSVACPYNARYKVNFAEPAYGDRLM 120
           CDEPPC  VCPTTAT KRADG+V IDYD+CIGC YC VACPY ARYKV+    A+ D+  
Sbjct: 61  CDEPPCRDVCPTTATTKRADGMVMIDYDICIGCGYCIVACPYQARYKVSKPTFAFKDQET 120

Query: 121 ANEKQRADPARVGVATKCTFCSDRIDYGVAHGLTPGVDPDATPACANACIANALTFGDID 180
            NE+ R D   +GVA KCTFC DR+DYG+A+GLTPGV P+ATPAC N+C++ ALTFGD D
Sbjct: 121 QNERTRFDERLLGVAQKCTFCVDRVDYGLANGLTPGVAPEATPACVNSCLSKALTFGDTD 180

Query: 181 DPNSKASRLLRENEHFRMHEELGTGPGFFYLWE 213
           +P+S  S+LL+  + FRMHEELGTGP   YLWE
Sbjct: 181 NPDSNVSKLLKRYKSFRMHEELGTGPNIHYLWE 213


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: 321
Number of extensions: 15
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: 215
Length of database: 217
Length adjustment: 22
Effective length of query: 193
Effective length of database: 195
Effective search space:    37635
Effective search space used:    37635
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: 45 (21.9 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