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 207020 DVU1570 pyruvate ferredoxin oxidoreductase, beta subunit

Query= uniprot:OFOB1_SULTO
         (305 letters)



>MicrobesOnline__882:207020
          Length = 284

 Score =  214 bits (546), Expect = 1e-60
 Identities = 111/258 (43%), Positives = 164/258 (63%), Gaps = 14/258 (5%)

Query: 11  WCPGCGNFGILNAEQQAIVELGVDTKNVVVVSGIGCSGKIPHFFRTPISGVHTLHGRAIA 70
           WCPGCGN  I+ A +QAIV LG++   V  VSGIG + K PH+ R  ++G + LHGR++ 
Sbjct: 15  WCPGCGNHDIMKALRQAIVGLGLEAHKVAHVSGIGQAAKAPHYIR--LNGFNGLHGRSLP 72

Query: 71  FATGIKLSNPDLVVIVNGGDGDLLGIGAGHFVAAGRRNVDMVVILHDNGVYGLTKGQASP 130
            A  I+L N +L VI   GDG   G G  HF+AA RRNVDM +++HDN +YGLTKGQASP
Sbjct: 73  PAQAIRLCNSELTVIAQSGDGCNYGEGGNHFLAAIRRNVDMTLLVHDNQIYGLTKGQASP 132

Query: 131 TLKRGEKPKSLPRPNINDAVNPIALAISSGYTFVARGYAYDVKHLKELIKSAIKHKGLAL 190
           T   G+  KS P    +   NP+A+A++    FVAR ++ +V+HL+ +I++A++H+G +L
Sbjct: 133 TTGEGQVTKSQPGGVTSAPFNPVAVAVAMRCGFVARSFSGNVEHLQAMIEAAVRHRGFSL 192

Query: 191 IDVLQPCPTYNDINTKEWYDKRIYKLDTLPDWDPVVKKPEEVNEKIKRAIDKSLEWGDRI 250
           +D+  PC ++N +NT  WY +R  ++D   D       P + N  ++ A      +GD +
Sbjct: 193 VDIFSPCVSFNKVNTFGWYRQRCREIDASHD-------PTDWNAAMRIAD----TFGDVL 241

Query: 251 PIGIFYQNELVPSYEERI 268
           PIG+ Y+NE  P  +ER+
Sbjct: 242 PIGVIYRNER-PPLDERV 258


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: 215
Number of extensions: 11
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: 284
Length adjustment: 26
Effective length of query: 279
Effective length of database: 258
Effective search space:    71982
Effective search space used:    71982
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