GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuD in Rhodobacter ovatus JA234

Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_097029019.1 CRO07_RS00205 acyl-CoA carboxylase subunit beta

Query= BRENDA::Q9LDD8
         (587 letters)



>NCBI__GCF_900207575.1:WP_097029019.1
          Length = 510

 Score =  263 bits (673), Expect = 1e-74
 Identities = 172/522 (32%), Positives = 267/522 (51%), Gaps = 32/522 (6%)

Query: 68  MEGILSELRSHIKKVLAGGGEEAVKRNRSRNKLLPRERIDRLLDPGSSFLELSQLAGHEL 127
           M+ IL EL        AGGG+  V+    R KL  RERID LLD GS F E      H  
Sbjct: 1   MKDILQELEDRRAIARAGGGQRRVEAQHKRGKLTARERIDLLLDEGS-FEEFDMFVRHRC 59

Query: 128 ----YEEPLPSG-GIITGIGPIHGRICMFMANDPTVKGGTYYPITIKKHLRAQEIAARCR 182
                E+  P+G G++TG G I+GR+    + D TV GG+      +K  +  ++A +  
Sbjct: 60  TDFGMEDDRPAGDGVVTGWGTINGRMVYVFSQDFTVFGGSLSETHAQKICKIMDMAMQNG 119

Query: 183 LPCIYLVDSGGAYLPKQAEVFPDKENFGRVFYNESVMSSDGIPQIAIVLGSCTAGGAYIP 242
            P I L DSGGA +    E       +  VF   ++M+S  IPQI++++G C  G  Y P
Sbjct: 120 APVIGLNDSGGARIQ---EGVASLAGYADVF-QRNIMASGVIPQISVIMGPCAGGAVYSP 175

Query: 243 AMADESVMVKGNGTIFLAGPPLVKAATGEEVSAEDLGGATVHCTVSGVSDYFAQDELHGL 302
           AM D   MV+    +F+ GP +VK  T E V+AE+LGGA+ H   S V+D   ++++  L
Sbjct: 176 AMTDFIFMVRDTSYMFVTGPDVVKTVTNEVVTAEELGGASTHTKKSSVADGAFENDVEAL 235

Query: 303 AIGRNIVKNLHMAAKQGMEGTFGSKNLVYKEPLYDINELRSIAPVDHKQQFDVRSIIARI 362
           A  R +V  L ++ +     T       + +     + L ++ P +  Q +D++ +I +I
Sbjct: 236 AEIRRLVDFLPLSNR-----TPAPVRPFFDDVARVEDSLDTLIPDNPNQPYDMKELILKI 290

Query: 363 VDGSEFDEFKKQYGTTLVTGFARIYGQTVGIIGNN-----GILFNESALKGAHFIELCSQ 417
            D  +F E +K Y   ++TGF R+ GQ+VG++ N      G L  +S+ K A F+  C  
Sbjct: 291 ADEGDFYEIQKDYAANIITGFIRLEGQSVGVVANQPMVLAGCLDIDSSRKAARFVRFCDA 350

Query: 418 RKIPLVFLQNITGFMVGSRAEANGIAKAGAKMVMAVSCAKVPKITIITGASFGAGNYAMC 477
             IP++ L ++ GF+ G+  E  G+ K GAK++ A   A VPK+T+IT  ++G     M 
Sbjct: 351 FNIPILTLVDVPGFLPGTGQEYGGVIKHGAKLLFAYGEATVPKVTVITRKAYGGAYDVMS 410

Query: 478 GRAYSPDFMFIWPNARIGIMGGAQAAGVLTQIERATKKRQGIKWTEEEEEAFKKKTVDAY 537
            +    DF + WP A I +MG   A  +L + E A K++   + T+E E+ F        
Sbjct: 411 SKHLRGDFNYAWPTAEIAVMGAKGATEILYRAELADKEKIAAR-TKEYEDRF-------- 461

Query: 538 EREANPYYSTARLWDDGVIDPCDTRKVLGLCLSAALNRPLED 579
              ANP+ +  R + D VI P  TR+ +    ++  N+ L +
Sbjct: 462 ---ANPFVAAERGFIDEVIMPHSTRRRVSRAFASLRNKKLSN 500


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: 700
Number of extensions: 31
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: 510
Length adjustment: 36
Effective length of query: 551
Effective length of database: 474
Effective search space:   261174
Effective search space used:   261174
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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