GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ofoB in Amycolatopsis halophila YIM 93223

Align 2-oxoacid:ferredoxin oxidoreductase subunit beta; OFOR; EC 1.2.7.11 (characterized)
to candidate WP_034267069.1 AMYHA_RS01155 2-oxoacid:ferredoxin oxidoreductase subunit beta

Query= SwissProt::P72579
         (305 letters)



>NCBI__GCF_000504245.1:WP_034267069.1
          Length = 355

 Score =  185 bits (469), Expect = 2e-51
 Identities = 97/225 (43%), Positives = 140/225 (62%), Gaps = 10/225 (4%)

Query: 11  WCPGCGNFGILNAEQQAIVELGVDTKNVVVVSGIGCSGKIPHFFRTPISGVHTLHGRAIA 70
           WCPGCG++ +LN  Q  +  LG+  +N+V VSGIGCS + P++  T   G+H++HGRA A
Sbjct: 39  WCPGCGDYIVLNTMQSFLPTLGLKPENIVFVSGIGCSSRFPYYMNT--YGMHSIHGRAPA 96

Query: 71  FATGIKLSNPDLVVIVNGGDGDLLGIGAGHFVAAGRRNVDMVVILHDNGVYGLTKGQASP 130
            ATG+  S PDL V V  GDGD L IG  H + A RRNV+  ++L +N +YGLTKGQ SP
Sbjct: 97  IATGLATSRPDLSVWVITGDGDALSIGGNHLIHALRRNVNFKILLFNNRIYGLTKGQYSP 156

Query: 131 TLKRGEKPKSLPRPNINDAVNPIALAISSGYTFVARGYAYDVKHLKELIKSAIKHKGLAL 190
           T + G + KS P  +++   NPI+LA+ +  +FV R    D K L E++ +A +H+G A 
Sbjct: 157 TSQEGMRTKSTPMGSLDHPFNPISLALGAEASFVGRALDSDKKGLTEVLTAAAQHRGSAF 216

Query: 191 IDVLQPCPTYND-----INTKEWYDKRIYKLDTLPDWDPVVKKPE 230
           +++ Q CP +ND     +  K+   +RI  L   PD +P+   PE
Sbjct: 217 VEIYQNCPIFNDGAFDVLKDKDEAARRIIPL--RPD-EPITFGPE 258


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: 276
Number of extensions: 14
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: 305
Length of database: 355
Length adjustment: 28
Effective length of query: 277
Effective length of database: 327
Effective search space:    90579
Effective search space used:    90579
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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