GapMind for catabolism of small carbon sources

 

Aligments for a candidate for padC in Pedobacter sp. GW460-11-11-14-LB5

Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate CA265_RS17845 CA265_RS17845 molybdopterin oxidoreductase

Query= uniprot:A0A2R4BLY8
         (215 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS17845 CA265_RS17845
           molybdopterin oxidoreductase
          Length = 1010

 Score =  122 bits (307), Expect = 2e-32
 Identities = 79/246 (32%), Positives = 104/246 (42%), Gaps = 38/246 (15%)

Query: 4   YAMVADLRRCVGCQTCTAACKHTNATPP--------GVQWRWVL---------------- 39
           + M  DL  C GC +C  AC   N  P           +  W+                 
Sbjct: 753 WVMAIDLNACTGCGSCIVACNVENNIPVVGRDEVRRRREMHWIRIDRYYSYETKDGDVTR 812

Query: 40  DVEAGEFPDVSRTFV---PVGCQHCDEPPCETVCPTTATKKRADGLVTIDYDLCIGCAYC 96
           + E  +  D+    V   P+ CQHCD  PCETVCP  AT   +DGL  + Y+ C+G  YC
Sbjct: 813 EKEIAKLEDLDHVSVVHQPMLCQHCDHAPCETVCPVLATVHSSDGLNHMAYNRCVGTRYC 872

Query: 97  SVACPYNAR--YKVNFAEPAYGDRLMANE------KQRADPARVGVATKCTFCSDRIDYG 148
           +  CPY  R     N+   +  D  + NE               GV  KC+ C  RI  G
Sbjct: 873 ANNCPYKVRRFNWFNYWNDSRFDNYLNNEFTQLVLNPDVTTRSRGVMEKCSMCIQRIQGG 932

Query: 149 VAHG---LTPGVDPDATPACANACIANALTFGDIDDPNSKASRLLRENEHFRMHEELGTG 205
                    P  D D   AC  AC ANA+ FGD +DPNS+ S+ LR    + + EE+   
Sbjct: 933 KLQAKLEKRPLKDGDIKMACQEACSANAIVFGDANDPNSEVSKALRSERIYYVLEEINVK 992

Query: 206 PGFFYL 211
           PG  Y+
Sbjct: 993 PGIGYM 998


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: 533
Number of extensions: 19
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 215
Length of database: 1010
Length adjustment: 33
Effective length of query: 182
Effective length of database: 977
Effective search space:   177814
Effective search space used:   177814
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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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