Alignments for a candidate for ofoa in Steroidobacter denitrificans DSM 18526

GapMind for Amino acid biosynthesis

Alignments for a candidate for ofoa in Steroidobacter denitrificans DSM 18526

Align 2-oxoacid:ferredoxin oxidoreductase 2, subunit alpha; OFOR2; EC 1.2.7.11 (characterized)
to candidate WP_066922391.1 ACG33_RS14950 2-oxoacid:acceptor oxidoreductase subunit alpha

Query= SwissProt::Q9YBX7
         (642 letters)



>NCBI__GCF_001579945.1:WP_066922391.1
          Length = 625

 Score =  241 bits (616), Expect = 5e-68
 Identities = 191/640 (29%), Positives = 300/640 (46%), Gaps = 72/640 (11%)

Query: 3   DISLIIGGPQGGGIESAGQIAIKSMVLLGYEVLGSREYHSNIMGAHSYYHLRVQQHRPRS 62
           D  + +    G G  SA  + +KS+  +G  V+G   + SNI G  ++Y +RV +    +
Sbjct: 13  DFVVKLANVNGTGSASANTLVMKSIFRMGIPVIGKNYFPSNIQGLPTWYEIRVTREGHAA 72

Query: 63  LKLPVDGVLALDAESVFTHFRDVRPGGILVYD---PGTKSTRVDAIQPMAGPLKKRLKSL 119
               VD ++A++AE+     +DV  GG L++D   P     + D I  +  PL +     
Sbjct: 73  RSSRVDLMVAMNAETYAKDVKDVSAGGYLIFDSTWPRPMLLKRDDITILGAPLARMCNET 132

Query: 120 FDSRGMQPVVESAVKLAEEAGARIVGLPLKEMLKTLSERTGAPVARVSRALNTLGLASML 179
           F        V S + L     A ++G                                  
Sbjct: 133 FQG------VRSRILLKNIMYAGLLGA--------------------------------- 153

Query: 180 YMLGVPVEYIEKAISLQFAGKEKVINMNVEAVRIAVDYVREAFGEP-ESRLPPGPRRGQT 238
            +L + ++ +   +   +A K+ +++ N++A+ I  +Y +E F  P   RL P  +    
Sbjct: 154 -LLDIDLQIMRTLLGESYANKKALLDSNIQALEIGYNYAKEHFTCPLPLRLEPMDKTSNH 212

Query: 239 MMVATGNDLVAMGKIVGGLGVITYYPITPSSDEALYVEKHSYISIDGPLAEKLGYDKIA- 297
           +++  GN    +G +  G  V  +YPITPS+         S +       +K   D    
Sbjct: 213 ILI-DGNTAAGLGCLYAGATVGAWYPITPST---------SIMDTFKSFCQKWRVDAQTG 262

Query: 298 ---VAIVQMEDELASINAVLGAAAAGARASTTTSGPGFSLMNEAVSLAVEAEIPVVVTLW 354
                IVQ EDELA+I AV+GA+  GARA T TSGPG SLMNE + LA  AEIP V+   
Sbjct: 263 ENDFVIVQCEDELAAIGAVIGASWNGARAFTPTSGPGISLMNEFIGLAYYAEIPAVIMDV 322

Query: 355 MRAGPSTGMPTRTGQQDLLHSIFSGHGDAPKIVLASGDHVEAFYDAIKAFNWAEEFQTPV 414
            R GPSTGMPTRT Q DL+ + ++ HGD   ++L   +  E FY +++AF+ AE  QTPV
Sbjct: 323 QRVGPSTGMPTRTQQCDLMLAAYASHGDTRHVLLFPSNPEECFYLSVQAFDLAERLQTPV 382

Query: 415 IHLLDKYLASS---MVSLARED-LDPSKVPITRGKLLDNPPADYRRYEVVEDGISPRARL 470
             + D  +  +     +LA +D   P +  +   + ++     YR ++   D I  R   
Sbjct: 383 FLMSDLDIGMNDWMCTNLAWDDEYQPDRGKVLSKEQIEKLDKFYRFFDHDGDAIPYRTLP 442

Query: 471 G---SATMVITGLEHDEYGYATEDPVMREIMMFKRERKFKVIEERIPDEEKAVLHGDSEA 527
           G          G  H++YG  TED    +I++ + +RKF   +  +P+   AVL GD   
Sbjct: 443 GVHPKGAYFTRGSGHNQYGGYTEDATEYQIVVDRLKRKFDTAKTLVPE---AVLTGDGTH 499

Query: 528 SVALVSFGSTKQPILEALEMLRDEGVRARFAQVRLLYPFPGRLVEEMLEGVEKVIMVEQN 587
           +  ++S GS    I EAL +L  +G++  + +VR  +PF G  VE  L     V +VEQN
Sbjct: 500 ATGIISLGSCDGAIQEALTLLERQGIQLDYLRVR-AFPF-GEDVEAFLAAHSLVFVVEQN 557

Query: 588 LLGQLAMLLRAHTSIKPD--SSIVKINGRPLYSFEVAGAV 625
              Q   LL   T ++ +  SSI+  +G P+ S  V   +
Sbjct: 558 RDAQFKSLLTLETRVEKEKLSSILYYSGLPMASDVVVDGI 597


Lambda     K      H
   0.318    0.135    0.380 

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: 819
Number of extensions: 41
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 642
Length of database: 625
Length adjustment: 38
Effective length of query: 604
Effective length of database: 587
Effective search space:   354548
Effective search space used:   354548
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: 54 (25.4 bits)

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

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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:

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