GapMind for catabolism of small carbon sources

 

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

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_011386482.1 AMB_RS20905 enoyl-CoA hydratase/carnithine racemase

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>NCBI__GCF_000009985.1:WP_011386482.1
          Length = 254

 Score =  126 bits (317), Expect = 4e-34
 Identities = 79/252 (31%), Positives = 124/252 (49%), Gaps = 4/252 (1%)

Query: 4   ENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAA 63
           E +L    G V +V +NRP   NAL   +   L  A  + +ADD +   ++ GS+  F+A
Sbjct: 3   ELVLSHVEGGVQVVRMNRPDKKNALIGEMYAALAEAFAKGEADDDVNVFLILGSQTDFSA 62

Query: 64  GADIGMMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFAA 123
           G D+    T+   +   G    R    V   RKP++AAV G A+G G  L   CD+++AA
Sbjct: 63  GNDLPDFLTW---EALSGSVADRFIRAVAGARKPVVAAVRGAAIGIGSTLLPHCDLVYAA 119

Query: 124 DTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIPA 183
              +F  P I LGI+P AG +Q +P      +A ++ +         AE  GL++ V+P 
Sbjct: 120 PGTRFHMPFINLGIVPEAGSSQTMPALAGHRRAAEMLMLGEPFGVDTAEAVGLINGVVPG 179

Query: 184 ASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQKEG 243
             L + A+AAA  +A  P   ++ +K  +    E  + + +  E  +F +    E   E 
Sbjct: 180 EDLEETAMAAARKLAAKPRSILVQIKALMKTPAE-PIMDRLTREAAVFDTCLKGEALNEA 238

Query: 244 MAAFVEKRKPVF 255
           ++AF EKR P F
Sbjct: 239 VSAFKEKRAPDF 250


Lambda     K      H
   0.321    0.134    0.380 

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: 155
Number of extensions: 11
Number of successful extensions: 3
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: 258
Length of database: 254
Length adjustment: 24
Effective length of query: 234
Effective length of database: 230
Effective search space:    53820
Effective search space used:    53820
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