GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuD in Pedobacter sp. GW460-11-11-14-LB5

Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate CA265_RS16635 CA265_RS16635 methylmalonyl-CoA carboxyltransferase

Query= BRENDA::Q9LDD8
         (587 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS16635 CA265_RS16635
           methylmalonyl-CoA carboxyltransferase
          Length = 513

 Score =  256 bits (655), Expect = 1e-72
 Identities = 163/505 (32%), Positives = 259/505 (51%), Gaps = 29/505 (5%)

Query: 68  MEGILSELRSHIKKVLAGGGEEAVKRNRSRNKLLPRERIDRLLDPGSSFLELSQLAGHE- 126
           M+  ++ L+  I +   GGG+  +     + KL  RERI  L+D GS F E+  +  H  
Sbjct: 1   MDKKIALLKDKINQANLGGGQARIDSQHKKGKLTARERIHFLMDEGS-FEEIGMMVTHRS 59

Query: 127 ----LYEEPLPSGGIITGIGPIHGRICMFMANDPTVKGGTYYPITIKKHLRAQEIAARCR 182
               +  E     G++TG G + GR+    + D TV GG+      +K  +  ++A +  
Sbjct: 60  TDFGMEREKYLGDGVVTGYGTVSGRLTYVFSQDFTVFGGSLSETHAEKICKLMDMAMKNG 119

Query: 183 LPCIYLVDSGGAYLPKQAEVFPDKENFGRVFYNESVMSSDGIPQIAIVLGSCTAGGAYIP 242
            P I L DSGGA +    E       +  +FY ++V +S  IPQ++ ++G C  G  Y P
Sbjct: 120 APLIGLNDSGGARIQ---EGVVSLGGYADIFY-KNVQASGVIPQLSAIMGPCAGGAVYSP 175

Query: 243 AMADESVMVKGNGTIFLAGPPLVKAATGEEVSAEDLGGATVHCTVSGVSDYFAQDELHGL 302
           A+ D  +MV+    +F+ GP +VK  T EEV++E+LGGA+ H T SGV+ +   +E+  +
Sbjct: 176 AITDFILMVENTSYMFVTGPNVVKTVTHEEVTSEELGGASTHATKSGVTHFACANEIEAI 235

Query: 303 AIGRNIVKNLHMAAKQGMEGTFGSKNLVYKEPLYDINELRSIAPVDHKQQFDVRSIIARI 362
               N +K L     Q  E    + +L Y+       EL +  P +  Q +D+R +I+ +
Sbjct: 236 ----NHLKKLLSYMPQNCEEI--ADHLPYETADESRPELNTFMPENASQPYDIREVISAV 289

Query: 363 VDGSEFDEFKKQYGTTLVTGFARIYGQTVGIIGNN-----GILFNESALKGAHFIELCSQ 417
            D   F E    Y   +V GFAR+ G+++GI+ N      G+L + S+ K A F+  C  
Sbjct: 290 ADTDSFLEVHAAYAENIVVGFARLAGRSIGIVANQPAYLAGVLDSNSSTKAARFVRFCDC 349

Query: 418 RKIPLVFLQNITGFMVGSRAEANGIAKAGAKMVMAVSCAKVPKITIITGASFGAGNYAMC 477
             IPL+  +++ GF+ G+  E NGI   GAK++ A S A VP+IT+IT  ++G     M 
Sbjct: 350 FNIPLLVFEDVPGFLPGTDQEWNGIITNGAKLLYAFSEATVPRITVITRKAYGGAYDVMN 409

Query: 478 GRAYSPDFMFIWPNARIGIMGGAQAAGVLTQIERATKKRQGIKWTEEEEEAFKKKTVDAY 537
            +    D  + WP+A I +MG   AA ++ + E  + ++   KW E+E     K   D +
Sbjct: 410 SKHIGADMNYAWPSAEIAVMGAKGAAEIIFKREITSAEKPEEKWLEKE-----KLYSDIF 464

Query: 538 EREANPYYSTARLWDDGVIDPCDTR 562
              ANPY +  R + D VI+P  TR
Sbjct: 465 ---ANPYRAAERGFVDEVIEPAQTR 486


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: 721
Number of extensions: 33
Number of successful extensions: 6
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: 513
Length adjustment: 36
Effective length of query: 551
Effective length of database: 477
Effective search space:   262827
Effective search space used:   262827
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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