GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS17845
          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:

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