GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ofoB in Desulfovibrio vulgaris Miyazaki F

Align 2-oxoacid:ferredoxin oxidoreductase subunit beta; OFOR; EC 1.2.7.11 (characterized)
to candidate 8499839 DvMF_0604 2-oxoglutarate ferredoxin oxidoreductase subunit beta (RefSeq)

Query= SwissProt::P72579
         (305 letters)



>FitnessBrowser__Miya:8499839
          Length = 277

 Score =  160 bits (406), Expect = 2e-44
 Identities = 94/265 (35%), Positives = 145/265 (54%), Gaps = 30/265 (11%)

Query: 11  WCPGCGNFGILNAEQQAIVELGVDTKNVVVVSGIGCSGKIPHFFRTPISGVHTLHGRAIA 70
           +C GCG+  +L +  +++  LG+   +VV+V+GIGCSG++  +     + VHT HGRA+ 
Sbjct: 22  FCAGCGHGIVLGSLIRSVHALGLPKDDVVLVAGIGCSGRMAVY--VDFNTVHTTHGRALT 79

Query: 71  FATGIKLSNPDLVVIVNGGDGDLLGIGAGHFVAAGRRNVDMVVILHDNGVYGLTKGQASP 130
           FATGIK++NP L VI   GDGD L IG  H + A RRN+ +  ++ +N +YG+T GQ S 
Sbjct: 80  FATGIKMANPKLKVICVMGDGDALSIGGNHLIHAARRNIGVTALILNNQIYGMTGGQCSS 139

Query: 131 TLKRGEKPKSLPRPNINDAVNPIALAISSGYTFVARGYAYDVKHLKELIKSAIKHKGLAL 190
              +G+   + P  ++  A +   +  ++G ++VARG ++    L  LI SAI H G ++
Sbjct: 140 ATPQGDISMTTPFGSLEKAFDIADMCKAAGASYVARGTSFHAIQLDRLISSAIMHPGFSV 199

Query: 191 IDVLQPCPTY--------NDINTKEWYDKRIYKLDTLPDWDPVVKKPEEVNEKIKRAIDK 242
           ++V  PCPT         N ++  +W      K++TL D D   +KP +           
Sbjct: 200 VEVFSPCPTQYGRKNKFRNAVDMYKWLKSNTVKVETLKDPD---QKPAD----------- 245

Query: 243 SLEWGDRIPIGIFYQNELVPSYEER 267
                 RIPIG+F   E  P  EER
Sbjct: 246 -----GRIPIGVFRDVE-EPGLEER 264


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: 191
Number of extensions: 8
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: 277
Length adjustment: 26
Effective length of query: 279
Effective length of database: 251
Effective search space:    70029
Effective search space used:    70029
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.

Links

Downloads

Related tools

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