GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS16635
          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:

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