Alignments for a candidate for ofoa in Sulfuritalea hydrogenivorans DSM 22779

GapMind for Amino acid biosynthesis

Alignments for a candidate for ofoa in Sulfuritalea hydrogenivorans DSM 22779

Align 2-oxoacid:ferredoxin oxidoreductase 2, subunit alpha; OFOR2; EC 1.2.7.11 (characterized)
to candidate WP_041100122.1 SUTH_RS14075 2-oxoacid:acceptor oxidoreductase subunit alpha

Query= SwissProt::Q9YBX7
         (642 letters)



>NCBI__GCF_000828635.1:WP_041100122.1
          Length = 616

 Score =  220 bits (560), Expect = 2e-61
 Identities = 190/643 (29%), Positives = 288/643 (44%), Gaps = 68/643 (10%)

Query: 3   DISLIIGGPQGGGIESAGQIAIKSMVLLGYEVLGSREYHSNIMGAHSYYHLRVQQHRPRS 62
           D  +      G G  SA ++  +S++ +G  V     + SNI G  ++Y +RV       
Sbjct: 12  DFVIKFANVNGSGSASANELFARSIMRMGVPVAPRNIFPSNIQGMPTWYEMRVSAAGWLG 71

Query: 63  LKLPVDGVLALDAESVFTHFRDVRPGGILVYDPGTKSTRVDAIQPMAGPLKKRLKSLFDS 122
            +   D ++A++ ++      ++  GG LVYD                      K+L  S
Sbjct: 72  RRGGCDLMVAMNPQTWDRDIAEIEAGGYLVYDS--------------------TKALPRS 111

Query: 123 RGMQPVVESAVKLAEEAGARIVGLPLKEMLKTLSERTGAPVARVSRALNTLGLASMLYML 182
           R    +              ++G+PL E+     E T     ++ +  N + + ++  +L
Sbjct: 112 RFRDDIT-------------VLGIPLTEICNR--EYTDPRQRQLFK--NIMYVGALTALL 154

Query: 183 GVPVEYIEKAISLQFAGKEKVINMNVEAVRIAVDYVREAFGEPES-RLPPGPRRGQTMMV 241
           G+    +EK I+ Q+ GK+K+I  NV A+++  DY RE    P   R+      G+ + +
Sbjct: 155 GMDFTVVEKLIADQYRGKDKLIGANVNALKLGYDYARENVSCPIGLRVERSDGVGEKIFI 214

Query: 242 ATGNDLVAMGKIVGGLGVITYYPITPSSDEALYVEKHSYISIDGPLAEKLGYDK----IA 297
             GND   +G + GG  V  +YPITPS+         S I   G    K   D       
Sbjct: 215 -NGNDACGLGAVYGGATVAGWYPITPST---------SVIEAFGSYCRKYRTDPDNGMAR 264

Query: 298 VAIVQMEDELASINAVLGAAAAGARASTTTSGPGFSLMNEAVSLAVEAEIPVVVTLWMRA 357
            AIVQ EDELASI  V+GAA  GARA T TSGPG SLM E   LA  AE+PVVV    R 
Sbjct: 265 YAIVQAEDELASIGMVIGAAWNGARAFTATSGPGISLMQEFFGLAYFAEVPVVVFNVQRG 324

Query: 358 GPSTGMPTRTGQQDLLHSIFSGHGDAPKIVLASGDHVEAFYDAIKAFNWAEEFQTPVIHL 417
           GPSTGMPTRT Q DL+   ++ HGD   ++L   D  E F    +AF+ AE  QTPV  +
Sbjct: 325 GPSTGMPTRTQQSDLIACAYASHGDTKHVLLFPEDPYECFTLGAQAFDLAERLQTPVFVM 384

Query: 418 LDKYLASSMVSLAREDLDPSKVPITRGKLLD----NPPADYRRY-EVVEDGIS----PRA 468
           LD  +  +       D D  +    RGK++         ++ RY +V  DGI     P  
Sbjct: 385 LDLDIGMNDRLCQPFDWDDQR-RYDRGKVMTAEELEAGKNFGRYLDVDGDGIPWRTIPGT 443

Query: 469 RLGSATMVITGLEHDEYGYATEDPVMREIMMFKRERKFKVIEERIPDEEKAVLHGDSEAS 528
                     G   + Y   +E        M +  RKF+  ++ +P     V        
Sbjct: 444 HPSKGAFFSRGTTRNAYAKYSEAGTDYVYNMERLRRKFETAKKLVP--APMVQRASQATR 501

Query: 529 VALVSFGSTKQPILEALEMLRDEGVRARFAQVRLLYPFPGRLVEEMLEGVEKVIMVEQNL 588
              + +GST   + EA  +L  +G+     +VR  +PF   ++E + E  + V +VEQN 
Sbjct: 502 FGAIYYGSTSPAMAEAYALLEAQGIHVDIMRVR-GFPFADEVIEFINEH-DHVFVVEQNE 559

Query: 589 LGQLAMLLRAHTSIKPDS--SIVKINGRPLYSFEVAGAVKRIL 629
            GQL MLL     + P     ++  +G P+ +  ++G +   L
Sbjct: 560 SGQLRMLLMNEGEVDPKRLIRVLHYDGTPITARFISGRIAAAL 602


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: 831
Number of extensions: 42
Number of successful extensions: 6
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: 616
Length adjustment: 38
Effective length of query: 604
Effective length of database: 578
Effective search space:   349112
Effective search space used:   349112
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 Apr 09 2024. The underlying query database was built on Apr 09 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 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 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