GapMind for catabolism of small carbon sources

 

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

Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate WP_011384008.1 AMB_RS08070 NAD(P)-dependent oxidoreductase

Query= uniprot:A0A4R8NY47
         (263 letters)



>NCBI__GCF_000009985.1:WP_011384008.1
          Length = 245

 Score = 63.9 bits (154), Expect = 3e-15
 Identities = 65/248 (26%), Positives = 98/248 (39%), Gaps = 19/248 (7%)

Query: 20  KRVVITGGGSGIGAALVEAFVGQGAQVCFLDIATEPSEALV-ASLKDAAVAPRFFPCNLM 78
           K VV+TG   GIG A+   F+ +G +V     A  P E ++  +     VA    P +  
Sbjct: 5   KTVVVTGASRGIGHAIARRFLAEGWRVITCARADVPKECMIDRNWACHIVADLADPASAQ 64

Query: 79  NLEALRATFTEIETVMGGVDILINNAANDDRHKSEDVTPAY------WDERLAVNLRHQF 132
           +  A    +   E +      L+NNA    +   ++           W +   +N     
Sbjct: 65  DFVAQANAWLGAEPLHA----LVNNAGVSPKTPYKERLGVLNGPIDGWKDVFELNFFAPL 120

Query: 133 FCAQAVLPGMRERKGGVILNFGSISWHLGLPDL-TLYMTAKAGIEGMTHGMARDFGRDGV 191
             A+     +   KG ++ N  SI+ H   P   + Y T+KA + G+T  MA +  + GV
Sbjct: 121 RLARGFASALHRGKGAIV-NITSIAGHYVHPFAGSAYSTSKAALSGLTREMAAEMAQLGV 179

Query: 192 RVNAIIPGAIRTPRQTLLWHTPEEEAKILAAQCLPVRVDPHDVAALALFLSSDSGAKCTG 251
           RVNA+ PG IRT           E   ++    L     P DVA     L        TG
Sbjct: 180 RVNAVAPGEIRTEM------ISAEYEALVPRIPLERMGTPEDVAGTVFRLCGSDFDYVTG 233

Query: 252 REYYVDAG 259
            E +V  G
Sbjct: 234 TEVFVTGG 241


Lambda     K      H
   0.322    0.137    0.417 

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: 158
Number of extensions: 10
Number of successful extensions: 2
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: 263
Length of database: 245
Length adjustment: 24
Effective length of query: 239
Effective length of database: 221
Effective search space:    52819
Effective search space used:    52819
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: 47 (22.7 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