GapMind for catabolism of small carbon sources

 

Aligments for a candidate for vorB in Bacteroides thetaiotaomicron VPI-5482

Align Ketoisovalerate oxidoreductase subunit VorB; VOR; 2-oxoisovalerate ferredoxin reductase subunit beta; 2-oxoisovalerate oxidoreductase beta chain; EC 1.2.7.7 (characterized)
to candidate 352363 BT2836 2-oxoglutarate synthase subunit korA (NCBI ptt file)

Query= SwissProt::P80908
         (352 letters)



>lcl|FitnessBrowser__Btheta:352363 BT2836 2-oxoglutarate synthase
           subunit korA (NCBI ptt file)
          Length = 616

 Score =  102 bits (254), Expect = 3e-26
 Identities = 99/382 (25%), Positives = 164/382 (42%), Gaps = 42/382 (10%)

Query: 6   VKGNTA----VIIGAMYAGCDCYFG-YPITPASEILHEASRYFPLVGRKFVQAESEEAAI 60
           + GN A    +I  A  AG + Y G YPITPA++ILHE +++  L G K VQ E E A  
Sbjct: 239 INGNKATSYGLIAAAEKAGLELYLGSYPITPATDILHELAKHKSL-GVKTVQCEDEIAGC 297

Query: 61  NMVYGAAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQAD 120
               GAA AG   +T +SGPG+ LK E ++     ELP VIV+V R GP  G   P +++
Sbjct: 298 ASAVGAAFAGALAVTTTSGPGICLKSEAMNLAVIGELPLVIVNVQRGGPSTGL--PTKSE 355

Query: 121 YNQLVKG--GGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEP 178
              L++   G +G     V+A  S     D    A ++A ++  PV++L DA +   +  
Sbjct: 356 QTDLLQALYGRNGESPMPVIAATSPTNCFDAAYMAAKIALEHMTPVVLLTDAFVANGSAA 415

Query: 179 LRFPE--------------------RAVEHRPDTS---WAVCGSRETM--------KNLV 207
            + P+                       +   +TS   WA  G+   M         N  
Sbjct: 416 WKLPDLNDYPAINPPYVTPDMAGNWTPYQRNEETSARYWATPGTEGFMHRIGGLEKSNET 475

Query: 208 TSIFLDFDELEEFNFYLQEKYAAVEENEVRYEEYMVEDAEIVLVAYGISSRVAKSAVDTA 267
            +I  + +   +     Q K   + +     E    EDA++++V +G +    + A+D  
Sbjct: 476 GAISTEPENHNKMVHLRQAKVDKIADYIPELEVLGDEDADLLIVGWGGTYGHLRLAMDFM 535

Query: 268 RADGIKVGLLRPITLFPFPSERIRELAEGGCTFISVEMSSGQMREDIKMASGCRDVELVN 327
           R  G KV       + P P +   ++       +  E + GQ    ++M     ++   N
Sbjct: 536 REHGKKVAFAHFQYINPLP-KNTADVLRKYKKIVVAEQNLGQFAGYLRMKVPGLNISQFN 594

Query: 328 RMGGNLIELRDILRKIREIAGE 349
           ++ G     R+++    ++  E
Sbjct: 595 QVKGQPFVTRELIDAFTKLLEE 616


Lambda     K      H
   0.319    0.136    0.390 

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: 457
Number of extensions: 19
Number of successful extensions: 3
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: 352
Length of database: 616
Length adjustment: 33
Effective length of query: 319
Effective length of database: 583
Effective search space:   185977
Effective search space used:   185977
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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