GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ofoA in Methanospirillum lacunae Ki8-1

Align 2-oxoacid:ferredoxin oxidoreductase subunit alpha; OFOR; EC 1.2.7.11 (characterized)
to candidate WP_109968409.1 DK846_RS07590 2-oxoacid:acceptor oxidoreductase subunit alpha

Query= SwissProt::P72578
         (632 letters)



>NCBI__GCF_003173355.1:WP_109968409.1
          Length = 365

 Score =  143 bits (361), Expect = 1e-38
 Identities = 103/333 (30%), Positives = 173/333 (51%), Gaps = 32/333 (9%)

Query: 232 LDGNTAVAIGKIYGGVRFQSYYPITPASDESVYIEAHQDVLMEDPITGDKKKGTIVVVQA 291
           + GN A A G +     F + YPITP+++ + ++ A             K+ G  +  Q 
Sbjct: 1   MQGNIACAEGALAADCTFFAGYPITPSTEVAEHMAAKLP----------KRNGCFI--QM 48

Query: 292 EDELAAINMAIGAALTGVRAATATSGPGFSLMVEGLGWAGMNEVPVVITYYIRGGPSTGL 351
           EDE+A++   IGAA TGVRA TATSGPGFSLM+E +G+A M+E P V+    RGGPSTG 
Sbjct: 49  EDEIASMAAIIGAAWTGVRAMTATSGPGFSLMMENIGYAVMSETPCVLVNVQRGGPSTGQ 108

Query: 352 PTRTAQSDLIFPIFAGHGEFPKIVLASGDHAEAFKDAIWALNLAEKYQTPVIHLVEKTLA 411
           PT  AQ D++   F  HG+F  I L+     E F+    A NLA++++ PV  + ++ + 
Sbjct: 109 PTMAAQGDMMQVRFGSHGDFSIIALSPSTVQECFELTAKAFNLADQFRCPVFVMADEVIG 168

Query: 412 NSYS--TIPYEELELDKLKAERGKIVESGDISYKRFKFTEDGISP--RAFLGKATMYYTG 467
           +     TIP      D +   R K ++   + +      E+ + P   AF     +  TG
Sbjct: 169 HMRERITIP------DSVPVVRAKPLKDDMLPFA----PEEDLIPGFAAFGTGRKIPVTG 218

Query: 468 DEHNEEGH-ISEDVVNRTMMYEKRMKKLEVADKEIPEESRVKIYGDLNSRNLIITWGSPT 526
             HNE+G+  S        +  + + K+E A   I +   V    + ++  + + +GSP 
Sbjct: 219 LTHNEKGYPDSTHPARHDSLVRRLVNKIENARHSIADYEIV----NQDAEYVFVCYGSPV 274

Query: 527 GVLRDILEESNFDFT-LLQIRMFSPFPKNLVSK 558
             ++++++ +    T  L++++  PFP++L+++
Sbjct: 275 RTVQEVVQRAKTPGTGYLKLKIVWPFPEDLLAR 307


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: 486
Number of extensions: 21
Number of successful extensions: 2
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: 365
Length adjustment: 34
Effective length of query: 598
Effective length of database: 331
Effective search space:   197938
Effective search space used:   197938
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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