GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuD in Bacteroides thetaiotaomicron VPI-5482

Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate 351214 BT1686 propionyl-CoA carboxylase beta chain (NCBI ptt file)

Query= BRENDA::Q9LDD8
         (587 letters)



>FitnessBrowser__Btheta:351214
          Length = 517

 Score =  264 bits (675), Expect = 6e-75
 Identities = 167/496 (33%), Positives = 251/496 (50%), Gaps = 44/496 (8%)

Query: 85  GGGEEAVKRNRSRNKLLPRERIDRLLDPGSSFLELSQLAGHE-----LYEEPLPSGGIIT 139
           GGGE+A+ +   + K   RERI  LLD GS F E+     H      + ++  P  G++T
Sbjct: 21  GGGEKAIAKQHEKGKYTARERIAMLLDEGS-FEEMDMFVEHRCTNFGMEKKHYPGDGVVT 79

Query: 140 GIGPIHGRICMFMANDPTVKGGTYYPITIKKHLRAQEIAARCRLPCIYLVDSGGAYLPKQ 199
           G G I GR+    A D TV  G+       K  +  + A +   PCI + DSGGA + + 
Sbjct: 80  GCGTIEGRLVYLFAQDFTVTAGSLSETMSLKICKIMDQAMKMGAPCIGINDSGGARIQEG 139

Query: 200 AEVFPDKENFGRVFYNESVMSSDGIPQIAIVLGSCTAGGAYIPAMADESVMVKGNGTIFL 259
                    +  +F   ++++S  IPQI+ + G C  G  Y PA+ D ++M++G   +FL
Sbjct: 140 INALA---GYAEIF-QRNILASGVIPQISGIFGPCAGGAVYSPALTDFTLMMEGTSYMFL 195

Query: 260 AGPPLVKAATGEEVSAEDLGGATVHCTVSGVSDYFAQDELHGLAIGRNIVKNLHMAAKQG 319
            GP +VK  TGE+VS E+LGGA+VH T SGV+ + A+ E  GLA+ R ++          
Sbjct: 196 TGPKVVKTVTGEDVSQENLGGASVHSTKSGVTHFTAKTEEEGLALIRTLL---------- 245

Query: 320 MEGTFGSKNLVYKEPLYDINE--------LRSIAPVDHKQQFDVRSIIARIVDGSEFDEF 371
              ++  +N + + P  D  +        L  I P    + +D+  +I+ IVD  EF E 
Sbjct: 246 ---SYIPQNNLEEAPYVDCTDPIDRLEDSLNDIIPDSPNKPYDMYEVISAIVDNGEFLEI 302

Query: 372 KKQYGTTLVTGFARIYGQTVGIIGNN-----GILFNESALKGAHFIELCSQRKIPLVFLQ 426
           +K Y   ++ GFAR  GQ+VGI+ N      G+L + ++ KGA F+  C    IP+V L 
Sbjct: 303 QKDYAKNIIIGFARFNGQSVGIVANQPKFLAGVLDSNASRKGARFVRFCDAFNIPIVSLV 362

Query: 427 NITGFMVGSRAEANGIAKAGAKMVMAVSCAKVPKITIITGASFGAGNYAMCGRAYSPDFM 486
           ++ GF+ G+  E NG+   GAK++ A   A VPK+TI    S+G  +  M  +    D  
Sbjct: 363 DVPGFLPGTGQEYNGVILHGAKLLYAYGEATVPKVTITLRKSYGGSHIVMSCKQLRGDMN 422

Query: 487 FIWPNARIGIMGGAQAAGVLTQIERATKKRQGIKWTEEEEEAFKKKTVDAYEREANPYYS 546
           + WP A I +MGGA A  VL   E   ++       E+E E  K          ANPY +
Sbjct: 423 YAWPTAEIAVMGGAGAVEVLYAREAKDQENPAQFLAEKEAEYTK--------LFANPYNA 474

Query: 547 TARLWDDGVIDPCDTR 562
               + D VI+P +TR
Sbjct: 475 AKYGYIDDVIEPRNTR 490


Lambda     K      H
   0.320    0.138    0.408 

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: 741
Number of extensions: 35
Number of successful extensions: 7
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: 587
Length of database: 517
Length adjustment: 36
Effective length of query: 551
Effective length of database: 481
Effective search space:   265031
Effective search space used:   265031
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: 53 (25.0 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:

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