GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ofoa in Desulfatibacillum aliphaticivorans DSM 15576

Align 2-oxoacid:ferredoxin oxidoreductase 1, subunit alpha; OFOR1; EC 1.2.7.11 (characterized)
to candidate WP_028313342.1 G491_RS0101620 2-oxoacid:acceptor oxidoreductase subunit alpha

Query= SwissProt::Q9YA13
         (639 letters)



>NCBI__GCF_000429905.1:WP_028313342.1
          Length = 383

 Score =  165 bits (417), Expect = 4e-45
 Identities = 116/352 (32%), Positives = 188/352 (53%), Gaps = 18/352 (5%)

Query: 239 SGEYVVASGNDVVAMGKVVGGVRYQAYYPITPASDESVLLEEFEGLKIDGESLGSIAILQ 298
           +GE+ + +G+   A G +  G  +   YPITPA++ +      E +      +G   I Q
Sbjct: 7   TGEHYM-TGDVACAEGALAAGCLFFGGYPITPATEVA------ERMSHRLPEIGGTYI-Q 58

Query: 299 TEDEIAAVSSVIGAALTGARASTATSGPGFSLMVEALGWAGKNDVPMVITYYQRGGPSTG 358
            EDEIAA++S++GA+  GA++ T+TSGPGFSLM+E LG A   + P V+   QR GPSTG
Sbjct: 59  MEDEIAAMASIVGASCAGAKSMTSTSGPGFSLMMENLGLAVITETPCVVVNVQRAGPSTG 118

Query: 359 LPTRGSQSDLLFSLFASHGEFPRIILSSGDHLEAFYDAIEAYNLAERFQMPVIHLLDKFL 418
           LPT+G+Q D++ + + SHG++  I ++     E FY  I+A+NLAE+++ PV+ + D+ +
Sbjct: 119 LPTQGAQGDMMQARWGSHGDYEIIAMAPASAQEIFYQTIDAFNLAEKYRTPVLIMTDEVI 178

Query: 419 ANMVASVPFPDWKAIK-IDRGKTLFKAPTGPFKRFPR-DQPLADRPVLGSGAITWYTGDE 476
            +M   V  PD + IK I+R K   K     ++ +   D  +      G G     TG  
Sbjct: 179 GHMSERVVIPDAREIKTIERVKA--KGRKDRYRPYAAGDLGVPPMANAGDGYKVHVTGLT 236

Query: 477 NDEYGHIDEDPVNRLVMYERRWKKMEIADREIPEDFRVKYYGDEDAEVLLVGWGSVKIPA 536
           +DE G+       +  M ER   K++    +I    R + +  EDA+ ++V +G      
Sbjct: 237 HDEMGYPAMTVEAQAAMMERLMGKIQNNRDDI---IRYEEFMIEDADYIIVTYGVSARTG 293

Query: 537 LEAIERLREMGVNAAYLHLRMLSPLPKRRVSEVLSRFDADRVIAVEANYLGQ 588
             A+E  R  G+    L L  + P  + ++ ++ S+  A  ++ VE N LGQ
Sbjct: 294 RAAVEEARAQGIKVGMLRLITVWPFAEEKIRDLASK--AKGMVTVEIN-LGQ 342


Lambda     K      H
   0.320    0.138    0.400 

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: 533
Number of extensions: 24
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: 639
Length of database: 383
Length adjustment: 34
Effective length of query: 605
Effective length of database: 349
Effective search space:   211145
Effective search space used:   211145
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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