Alignments for a candidate for ofoa in Hydrogenovibrio halophilus DSM 15072

GapMind for Amino acid biosynthesis

Alignments for a candidate for ofoa in Hydrogenovibrio halophilus DSM 15072

Align 2-oxoacid:ferredoxin oxidoreductase subunit alpha; OFOR; EC 1.2.7.11 (characterized)
to candidate WP_019896063.1 A377_RS0109295 2-oxoacid:acceptor oxidoreductase subunit alpha

Query= SwissProt::P72578
         (632 letters)



>NCBI__GCF_000384235.1:WP_019896063.1
          Length = 594

 Score =  201 bits (512), Expect = 6e-56
 Identities = 191/651 (29%), Positives = 287/651 (44%), Gaps = 106/651 (16%)

Query: 2   RLSWVIGGAQGTGIDTAANIFGNAVASAGYYIYGNREYYSNIKGGHSYFSLTISDKRVRS 61
           RLS  I GA G G  T   I   A   AG+Y    R +   I+GG S   L +SD+ + +
Sbjct: 16  RLSVSISGAGGAGAVTVGLILLEAFGKAGFYGAMTRSFGPQIRGGESAVFLNLSDQPIET 75

Query: 62  NTQKIDILVSFDAETVFQHFYDVKDILIYNKAVETTKIDAVQSMEPELAERIKDFLTKQG 121
             +  D+ ++ D +  F  F D           E       Q    +  E+    +   G
Sbjct: 76  LPEATDLHLALDWKN-FMRFAD-----------EIPLTSDTQIFYDDSREKPPQGVVDSG 123

Query: 122 YETTVKGALEYASKNNVTLIPVNYDEIAKKVADEMKVPLSVTERVKNIVGITISYKLLGL 181
            + T    +        TL  +    I                   N++G+ +  + LGL
Sbjct: 124 ADCTPLPLM-------TTLKQIQGGRI-------------------NMLGLGVIAQRLGL 157

Query: 182 DVNYLIEAINSTFKQDLYRKMNELAVKDSYDIVESRYNLKPSSK----------ERRRFW 231
              ++ +A+  T    L RK  E AV+ S + V     L  ++K          ++ R+ 
Sbjct: 158 ADTHIEQALQKT----LGRKGEE-AVRLSMETVRLGQTLVEAAKPSPLQNWQPTDKPRWH 212

Query: 232 LDGNTAVAIGKIYGGVRFQSYYPITPASDESVYIEAHQDVLMEDPITGDKKKGTIVVVQA 291
           L GN A AIG + GG++  + YPITPA+D   Y+    +          K+ G +++  A
Sbjct: 213 LSGNEACAIGALRGGLKLAAAYPITPATDIVEYLAPRIE----------KRGGQVLI--A 260

Query: 292 EDELAAINMAIGAALTGVRAATATSGPGFSLMVEGLGWAGMNEVPVVITYYIRGGPSTGL 351
           EDELAA+NM IG +  G  + TATSGPG +LM E +G A  +E P ++   +RGGPSTG+
Sbjct: 261 EDELAAMNMVIGGSFGGQPSMTATSGPGLALMTEAMGLAVASETPALVITVMRGGPSTGI 320

Query: 352 PTRTAQSDLIFPIFAGHGEFPKIVLASGDHAEAFKDAIWALNLAEKYQTPVIHLVEKTLA 411
           PT++ QSDL   ++  HGE P IV+A  + +E+     WAL LAE+ QT VI   ++ L 
Sbjct: 321 PTKSEQSDLNQILYGLHGEAPHIVVAPLNVSESVPVTQWALGLAERLQTLVILATDQHLG 380

Query: 412 NS---YSTIPYEELE----LDKLKAERGKIVESGDISYKRFKFTEDGISPRAFLGKATMY 464
            S       P+E++     L +L A       +    Y R+  T+ GISP    G     
Sbjct: 381 QSRLICDPSPFEDMAETRGLTRLLAH-----PNDPADYHRYALTDSGISPLTQPGMEHGA 435

Query: 465 YTGD--EHNEEGHISEDVVNRTMMYEKRMKKLEVADKEIPEESRVKIYGD--------LN 514
           YT D  EH E G  S    + +   EKR +KL   D           YGD          
Sbjct: 436 YTADGLEHTETGLPSSSASDHSAQTEKRARKLTEFD-----------YGDDWATYLPASK 484

Query: 515 SRNLIITWGSPTGVLRDILEESNFD------FTLLQIRMFSPFPKNLVSKLMEGRDKIIT 568
           S+ LIITWGS     +  +   N +      F+LL +R+  P   N + +L +G+ ++  
Sbjct: 485 SKRLIITWGSSFEACKQAVARHNAEAKKDEQFSLLGLRLLMPLQSNTLRQLCKGQ-QVFV 543

Query: 569 VEGNYLAQT-SLLVKMYTGKDVTNSILKWNGRPFLRDELEEALIKVIKDGE 618
           VE N   Q    L+        + SI +     F   EL   L ++ K+G+
Sbjct: 544 VEQNASGQLFHYLLSEQALPKSSQSIARSGPILFTPGELASTLRRLTKEGK 594


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: 730
Number of extensions: 30
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: 632
Length of database: 594
Length adjustment: 37
Effective length of query: 595
Effective length of database: 557
Effective search space:   331415
Effective search space used:   331415
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.

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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