GapMind for catabolism of small carbon sources

 

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

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate WP_011383249.1 AMB_RS04120 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase

Query= BRENDA::A0A076VF18
         (308 letters)



>NCBI__GCF_000009985.1:WP_011383249.1
          Length = 254

 Score = 98.6 bits (244), Expect = 1e-25
 Identities = 81/230 (35%), Positives = 107/230 (46%), Gaps = 26/230 (11%)

Query: 69  LSPLAPTDVPAIRGMGLQYSGDPANPQDKPPVACLFFKASQALAGPGDDIVLPRLARDEK 128
           L P+AP    A+    + Y+        K P   L F     L GPG  +    + R   
Sbjct: 39  LPPVAPGTTFAL---AINYADHAKELAFKAPEKPLAF-----LKGPGTFVGHRAVTRKPA 90

Query: 129 N----DYEVELCVVLGKDAKDVDEKDAMSFVGGYCVVNDVSSRGLCAKGGQWGMG-KSYD 183
           +     YE EL VV+G+ A+DV  KDA  FV GY V ND + R       +  +  K+ D
Sbjct: 91  DAGFMHYECELAVVIGRTARDVKAKDAYDFVAGYTVANDYAIRNFLQNYYRPNLRTKNRD 150

Query: 184 TWCPFGPCLVSPSALGADPHKLTITTHVNGKLAQKGNTADLVLKIPELIARLSHGTTLQA 243
                GP +V    + ADP  L I+T VNG   Q GNT D+V  +P LI  LS   TL  
Sbjct: 151 GCTVLGPWMVDRDDV-ADPMSLDISTFVNGARVQSGNTRDMVFGVPALIEYLSSFMTLSP 209

Query: 244 GSLILTGSPIALGRKAPGDAVEQSPFMKDGDEIRCFVEGCGTLINSVRDE 293
           G LILTG+P         D +     +K GDE+   VEG G L + + D+
Sbjct: 210 GDLILTGTP---------DGIVD---VKPGDEVVTEVEGVGRLTSFIVDD 247


Lambda     K      H
   0.316    0.135    0.411 

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: 230
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: 308
Length of database: 254
Length adjustment: 26
Effective length of query: 282
Effective length of database: 228
Effective search space:    64296
Effective search space used:    64296
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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