GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ofoa in Nitratiruptor tergarcus DSM 16512

Align 2-oxoacid:ferredoxin oxidoreductase 1, subunit alpha; OFOR1; EC 1.2.7.11 (characterized)
to candidate WP_084275835.1 B8779_RS07090 2-oxoglutarate synthase subunit alpha

Query= SwissProt::Q9YA13
         (639 letters)



>NCBI__GCF_900176045.1:WP_084275835.1
          Length = 382

 Score =  185 bits (470), Expect = 3e-51
 Identities = 126/390 (32%), Positives = 198/390 (50%), Gaps = 31/390 (7%)

Query: 243 VVASGNDVVAMGKVVGGVRYQAYYPITPASDE----SVLLEEFEGLKIDGESLGSIAILQ 298
           V++SGN++ A   +  G R+   YPITP+S+     SVLL    G             +Q
Sbjct: 5   VISSGNELAAKAAIDAGCRFFGGYPITPSSEVAHEMSVLLPRVGG-----------KFIQ 53

Query: 299 TEDEIAAVSSVIGAALTGARASTATSGPGFSLMVEALGWAGKNDVPMVITYYQRGGPSTG 358
            EDEI  ++  +GA+++G ++ T TSGPG SL  E +G     + P+VIT   RGGPSTG
Sbjct: 54  MEDEIGGIAVALGASMSGVKSMTNTSGPGISLKAEQIGLGFMTETPLVITNVMRGGPSTG 113

Query: 359 LPTRGSQSDLLFSLFASHGEFPRIILSSGDHLEAFYDAIEAYNLAERFQMPVIHLLDKFL 418
           LPTR  Q D+  +   +HG++  I    G   E + + + A+N+AE    PV  LLD+ L
Sbjct: 114 LPTRVQQGDINQAKAPTHGDYKSITFCPGSLEECYTEVVRAFNVAEELMTPVFVLLDETL 173

Query: 419 ANMVASVPFPDWKAIK---IDRGKTLFKAPTGPFKRF--PRDQPLADRPVLGSGAITWYT 473
            +M      PD + ++   +DR K     P   FK F  P+D+P A  P +  G     T
Sbjct: 174 GHMHGKAVLPDLEEVQASIVDRAKPDPSIPKEEFKPFDVPQDKP-AVIPPMFQGYRFHLT 232

Query: 474 GDENDEYGHIDEDPVNRLVMYERRWKKMEIADREIPEDFRVKYYGDEDAEVLLVGWGSVK 533
           G  +   G   ED      + ER  +K+++  +++ + +  + Y  +DAE L+V +GSV 
Sbjct: 233 GLHHGPTGFPTEDAEICQNLIERLHRKIDVRRKDLLDSY--EEYMLDDAEWLIVAYGSVS 290

Query: 534 IPALEAIERLREMGVNAAYLHLRMLSPLPKRRVSEVLSRFDADRVIAVEAN---YLGQAS 590
             A EAI RLR+ GV         L P P+ ++ E+  RF A++++  E N   Y+ +  
Sbjct: 291 RSAREAINRLRDQGVKIGMFRPITLWPSPEEKMKEIGERFPAEKILMPELNMGQYIDEVE 350

Query: 591 KIVTMETGFMFRKYILKWTGRPVYLHELVE 620
           +++           + K  GRP+   E++E
Sbjct: 351 RVMKKRP-----VALNKANGRPISPAEIIE 375


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: 569
Number of extensions: 23
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 639
Length of database: 382
Length adjustment: 34
Effective length of query: 605
Effective length of database: 348
Effective search space:   210540
Effective search space used:   210540
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.

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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:

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