Alignments for a candidate for ofoa in Desulfotalea psychrophila LSv54

GapMind for Amino acid biosynthesis

Alignments for a candidate for ofoa in Desulfotalea psychrophila LSv54

Align 2-oxoacid:ferredoxin oxidoreductase subunit alpha; OFOR; EC 1.2.7.11 (characterized)
to candidate WP_011189344.1 DP_RS10745 2-oxoacid:acceptor oxidoreductase subunit alpha

Query= SwissProt::P72578
         (632 letters)



>NCBI__GCF_000025945.1:WP_011189344.1
          Length = 566

 Score =  244 bits (622), Expect = 1e-68
 Identities = 188/627 (29%), Positives = 294/627 (46%), Gaps = 97/627 (15%)

Query: 6   VIGGAQGTGIDTAANIFGNAVASAGYYIYGNREYYSNIKGGHSYFSLTISDKRVRSNTQK 65
           V+GG  G GI        + V  +G Y++  +EY S ++GG +   + IS + VR++   
Sbjct: 10  VLGGEAGQGIQFLEKALLHIVKESGLYVFATKEYMSRVRGGINTTEIRISSEPVRAHVDV 69

Query: 66  IDILVSFDAETVFQHFYDVKDILIYNKAVETTKIDAVQSMEPELAERIKDFLTKQGYETT 125
           ID+L+             +K+ +I +     TK                         TT
Sbjct: 70  IDLLIP------------LKNGVIEHLGSRVTK------------------------STT 93

Query: 126 VKGALEYASKNNVTLIPVNYDEIAKKVADEMKVPLSVTERVKNIVGITISYKLLGLDVNY 185
           + G+ E+    +     +++   AKK  +++           N V +     LL  D   
Sbjct: 94  IVGSREHIGGRDTE---IDFAATAKKHGNQLYT---------NSVALGFLCGLLDFDSAN 141

Query: 186 LIEAINSTFKQDLYRKMNELAVKDSYDIVESRYNLKPSSKER----------------RR 229
           L + I  TF        +E  +  + D  E  Y +  +S  R                  
Sbjct: 142 LYKEIRDTFSLK-----SEGIIAGNIDAAEEGYKIGMASHSRLLTSGRPTPAKNRSLQEN 196

Query: 230 FWLDGNTAVAIGKIYGGVRFQSYYPITPASDESVYIEAHQDVLMEDPITGDKKKGTIVVV 289
             L+G  AVA+G + GG      YP+TP +  SV++           +    K+  IVV 
Sbjct: 197 LLLNGADAVALGAMAGGCNAAFAYPMTPGT--SVFLT----------LAEFSKQADIVVE 244

Query: 290 QAEDELAAINMAIGAALTGVRAATATSGPGFSLMVEGLGWAGMNEVPVVITYYIRGGPST 349
           Q EDE+  INMAIG+   G RA  +TSG GF+LM EG+  AGM E PVV+    R GP+T
Sbjct: 245 QVEDEIGVINMAIGSWYAGGRAIVSTSGGGFALMTEGISLAGMTETPVVVHLAQRPGPAT 304

Query: 350 GLPTRTAQSDLIFPIFAGHGEFPKIVLASGDHAEAFKDAIWALNLAEKYQTPVIHLVEKT 409
           GLPTRT Q DL   ++AGHGEF +++LA G   +AF+    A NLA+++Q PV  L ++ 
Sbjct: 305 GLPTRTEQGDLNLVLYAGHGEFARLILAPGTLEQAFEYTRLAFNLADRFQIPVFVLTDQF 364

Query: 410 LANSYSTIPYEELELDKLKAERGKIVESGDISYKRFKFTEDGISPRAF--LGKATMYYTG 467
             +SY  I +     D  + +    V   D SYKR++ +EDG+SPR     G   +    
Sbjct: 365 FVDSYYPIAHP----DAGQVQIESAVIKTDDSYKRYQLSEDGVSPRGIPGYGSGNVCLDS 420

Query: 468 DEHNEEGHISEDVVN-RTMMYEKRMKKLEVADKE--IPEESRVKIYGDLNSRNLIITWGS 524
           DEH+E+G I+ED+      M + R+KKLE   K   +PE     + G+ +   LII WGS
Sbjct: 421 DEHDEDGKITEDLDGIHLAMADNRLKKLETLTKAAMLPE-----LVGEPDYATLIIGWGS 475

Query: 525 PTGVLRDILE-ESNFDFTLLQIRMFSPFPKNLVSKLMEGRDKIITVEGNYLAQTSLLVKM 583
             G + + L+   +   + L      P  +  +++ ++G  K++ VE N L Q +  ++ 
Sbjct: 476 TYGAICEALQIIGSGKVSFLFCPQLYPLSEK-IAEYIDGAQKVVVVENNQLGQFADFLQR 534

Query: 584 YTGKDVTNSILKWNGRPFLRDELEEAL 610
             G+   + ILK+NG PF  +EL +++
Sbjct: 535 ELGRLFPHRILKYNGMPFSVEELVQSI 561


Lambda     K      H
   0.316    0.135    0.382 

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: 806
Number of extensions: 37
Number of successful extensions: 7
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: 632
Length of database: 566
Length adjustment: 37
Effective length of query: 595
Effective length of database: 529
Effective search space:   314755
Effective search space used:   314755
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 (21.6 bits)
S2: 53 (25.0 bits)

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original publication.

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

GapMind for Amino acid biosynthesis