GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuD in Amycolatopsis halophila YIM 93223

Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_034275130.1 AMYHA_RS25160 acyl-CoA carboxylase subunit beta

Query= BRENDA::Q9LDD8
         (587 letters)



>NCBI__GCF_000504245.1:WP_034275130.1
          Length = 549

 Score =  240 bits (612), Expect = 1e-67
 Identities = 162/527 (30%), Positives = 265/527 (50%), Gaps = 26/527 (4%)

Query: 51  PDGVDRNSEAFSSNSIAMEGILSELRSHIKKVLAGGGEEAVKRNRSRNKLLPRERIDRLL 110
           P G    S   S +     G L++L     + +  G   AV++  ++ K   RERID LL
Sbjct: 7   PLGGQHGSAEESIDIHTTAGKLADLYRRNDEAVHAGSARAVEKQHAKGKKTARERIDMLL 66

Query: 111 DPGSSFLELSQLAGHEL----YEEPLPSG-GIITGIGPIHGR-ICMFMANDPTVKGGTYY 164
           DPGS F+EL +LA H       +   P G G++TG G I GR +C+F + D T+ GG+  
Sbjct: 67  DPGS-FVELDELARHRSTNFGQDANRPYGDGVVTGYGTIDGRPVCVF-SQDVTIFGGSLG 124

Query: 165 PITIKKHLRAQEIAARCRLPCIYLVDSGGAYLPKQAEVFPDKENFGRVFYNESVMSSDGI 224
            +  +K ++  ++A +   P I + + GGA +    E       +G +F   +V +S  +
Sbjct: 125 EVYGEKIVKVMDLAIKTGRPIIGINEGGGARIQ---EGVVSLGLYGEIF-TRNVKASGVV 180

Query: 225 PQIAIVLGSCTAGGAYIPAMADESVMVKGNGTIFLAGPPLVKAATGEEVSAEDLGGATVH 284
           PQI++++G+   G  Y PA+ D  VMV     +F+ GP ++K  TGEEV+ E+LGG   H
Sbjct: 181 PQISLIMGANAGGHVYSPALTDFVVMVDQTSHMFITGPDVIKTVTGEEVTFEELGGGRSH 240

Query: 285 CTVSGVSDYFAQDELHGLAIGRNIVKNL---HMAAKQGMEGTFGSKNLVYKEPLYDINEL 341
            T SG + Y   DE   ++  + ++  L   ++A     E    + N V  +   D  EL
Sbjct: 241 NTKSGNAHYLGADEEDAISYVKELLSFLPPNNLAEPPVFEAPPHTGNSVADDITDDDREL 300

Query: 342 RSIAPVDHKQQFDVRSIIARIVDGSEFDEFKKQYGTTLVTGFARIYGQTVGIIGNN---- 397
            ++ P      +D+  +I  +VD  EF E  + +   ++ GF R+ GQ+VGI+ N     
Sbjct: 301 DTLIPDSPNVPYDMHEVITHVVDDGEFLEVHELFAPNVLVGFGRVDGQSVGIVANQPTQF 360

Query: 398 -GILFNESALKGAHFIELCSQRKIPLVFLQNITGFMVGSRAEANGIAKAGAKMVMAVSCA 456
            G L  +++ K A F+  C    +P++   ++ GF+ G+  E NGI + GAK++ A + A
Sbjct: 361 AGCLDIDASEKAARFVRTCDAFNVPVLTFVDVPGFLPGTDQEWNGIIRRGAKLIYAYAEA 420

Query: 457 KVPKITIITGASFGAGNYAMCGRAYSPDFMFIWPNARIGIMGGAQAAGVLTQIERATKKR 516
            VP +T+IT  ++G     M  +    D    WP A+I +MG   AA ++ +   A  + 
Sbjct: 421 TVPLVTVITRKAYGGAYDVMGSKHLGADINLAWPTAQIAVMGAQGAANIVYRKTLANAEA 480

Query: 517 QGIKWTEEEEEAFKKKTVDAYERE-ANPYYSTARLWDDGVIDPCDTR 562
           +G     ++ E  + + +  YE    NPY +  R + D VI P  TR
Sbjct: 481 EG-----QDIEKLRGELIQEYEDTLCNPYVAAERGYVDSVIPPSHTR 522


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: 756
Number of extensions: 45
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: 549
Length adjustment: 36
Effective length of query: 551
Effective length of database: 513
Effective search space:   282663
Effective search space used:   282663
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 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