GapMind for catabolism of small carbon sources

 

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

Align 2-oxoacid:ferredoxin oxidoreductase subunit beta; OFOR; EC 1.2.7.11 (characterized)
to candidate WP_011384545.1 AMB_RS10845 2-oxoglutarate synthase

Query= SwissProt::P72579
         (305 letters)



>NCBI__GCF_000009985.1:WP_011384545.1
          Length = 279

 Score =  176 bits (446), Expect = 6e-49
 Identities = 84/200 (42%), Positives = 127/200 (63%), Gaps = 5/200 (2%)

Query: 11  WCPGCGNFGILNAEQQAIVELGVDTKNVVVVSGIGCSGKIPHFFRTPISGVHTLHGRAIA 70
           WCPGCG++ +L++  +A  +LG+      VVSGIGCS +IP +  T   G+H++HGRA+A
Sbjct: 23  WCPGCGDYAVLSSITKAFADLGLKPHETSVVSGIGCSSRIPAYTNT--YGIHSIHGRALA 80

Query: 71  FATGIKLSNPDLVVIVNGGDGDLLGIGAGHFVAAGRRNVDMVVILHDNGVYGLTKGQASP 130
              G+KL+ PDL V+V GGDGD   IG  HF+ A RRNVD+  I+ DN VYG+TKGQ SP
Sbjct: 81  VGQGLKLARPDLTVMVAGGDGDGFSIGGNHFLHACRRNVDLTYIVMDNRVYGMTKGQPSP 140

Query: 131 TLKRGEKPKSLPRPNINDAV--NPIALAISSGYTFVARGYAYDVKHLKELIKSAIKHKGL 188
           T +      ++  P        +P+A+A++SG  F+ARG++ D     ++I  AI+H G 
Sbjct: 141 TTESDWDASAMAPPGGTGMTPFHPLAIALASGANFIARGFSGDPNGTAQIIAEAIRHPGF 200

Query: 189 ALIDVLQPCPTYNDINTKEW 208
           + + ++ PC T+ +   ++W
Sbjct: 201 SFVAIMSPCITFRE-EQRDW 219


Lambda     K      H
   0.318    0.139    0.424 

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: 213
Number of extensions: 9
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: 305
Length of database: 279
Length adjustment: 26
Effective length of query: 279
Effective length of database: 253
Effective search space:    70587
Effective search space used:    70587
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 (21.7 bits)
S2: 48 (23.1 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