GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ofob in Desulfovibrio vulgaris Hildenborough

Align 2-oxoacid:ferredoxin oxidoreductase 1, subunit beta; Short=OFOR1; EC 1.2.7.11 (characterized, see rationale)
to candidate 207416 DVU1946 pyruvate ferredoxin oxidoreductase, beta subunit, putative

Query= uniprot:OFOB1_SULTO
         (305 letters)



>MicrobesOnline__882:207416
          Length = 276

 Score =  164 bits (416), Expect = 2e-45
 Identities = 93/265 (35%), Positives = 149/265 (56%), Gaps = 31/265 (11%)

Query: 11  WCPGCGNFGILNAEQQAIVELGVDTKNVVVVSGIGCSGKIPHFFRTPISGVHTLHGRAIA 70
           +C GCG+  +L +  +++  LG+   +VVVV+GIGCSG++  +     + VHT HGRA+ 
Sbjct: 22  FCAGCGHGIVLGSLIRSVHALGLPKDDVVVVAGIGCSGRLAVY--VDFNTVHTTHGRALT 79

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

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

Query: 191 IDVLQPCPTY--------NDINTKEWYDKRIYKLDTLPDWDPVVKKPEEVNEKIKRAIDK 242
           ++V  PCPT         + ++  +W  K   K++TL + +    KPE+           
Sbjct: 200 VEVFSPCPTQYGRKNKFRSAVDMYKWLKKNTVKIETLKEGE----KPED----------- 244

Query: 243 SLEWGDRIPIGIFYQNELVPSYEER 267
                 RIPIG+F ++   P  EER
Sbjct: 245 -----GRIPIGVF-RDRQTPGLEER 263


Lambda     K      H
   0.318    0.139    0.425 

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: 201
Number of extensions: 12
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: 276
Length adjustment: 26
Effective length of query: 279
Effective length of database: 250
Effective search space:    69750
Effective search space used:    69750
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 Aug 03 2021. The underlying query database was built on Aug 03 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