GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ofoB in Sphingomonas koreensis DSMZ 15582

Align 2-oxoacid:ferredoxin oxidoreductase subunit beta; OFOR; EC 1.2.7.11 (characterized)
to candidate Ga0059261_0324 Ga0059261_0324 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, beta subunit

Query= SwissProt::P72579
         (305 letters)



>FitnessBrowser__Korea:Ga0059261_0324
          Length = 343

 Score =  178 bits (452), Expect = 1e-49
 Identities = 92/199 (46%), Positives = 127/199 (63%), Gaps = 5/199 (2%)

Query: 5   TPQWNDWCPGCGNFGILNAEQQAIVELGVDTKNVVVVSGIGCSGKIPHFFRTPISGVHTL 64
           T Q   WCPGCG++ IL A Q+ + E+G   +N V +SGIGCS + P++  T   G HT+
Sbjct: 17  TDQEVRWCPGCGDYAILKAVQRTMPEIGATPENTVFISGIGCSSRFPYYMET--YGFHTI 74

Query: 65  HGRAIAFATGIKLSNPDLVVIVNGGDGDLLGIGAGHFVAAGRRNVDMVVILHDNGVYGLT 124
           HGRA A ATG+KL+NPDL V +  GDGD L IG  H +   RRN++  V+L +N +YGLT
Sbjct: 75  HGRAPAVATGVKLANPDLDVWIITGDGDGLSIGGNHTMHLLRRNLNCQVLLFNNEIYGLT 134

Query: 125 KGQASPTLKRGEKPKSLPRPNINDAVNPIALAISSGYTFVARGYAYDV-KHLKELIKSAI 183
           KGQ SPT + G +  S P  +++    P A A+ SG  F+ARG   DV K+L  ++K+A 
Sbjct: 135 KGQYSPTSREGTRSPSTPFGSVDHPAKPCAYALGSGARFIARG--IDVHKNLPSVLKAAH 192

Query: 184 KHKGLALIDVLQPCPTYND 202
            H+G A +++ Q C  YND
Sbjct: 193 AHQGAAFVEIFQNCIVYND 211


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: 290
Number of extensions: 17
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: 343
Length adjustment: 28
Effective length of query: 277
Effective length of database: 315
Effective search space:    87255
Effective search space used:    87255
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