GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuD in Lacinutrix algicola AKS293

Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_055436809.1 ASC41_RS11575 acyl-CoA carboxylase subunit beta

Query= BRENDA::Q9LDD8
         (587 letters)



>NCBI__GCF_001418085.1:WP_055436809.1
          Length = 513

 Score =  268 bits (684), Expect = 5e-76
 Identities = 173/521 (33%), Positives = 266/521 (51%), Gaps = 29/521 (5%)

Query: 68  MEGILSELRSHIKKVLAGGGEEAVKRNRSRNKLLPRERIDRLLDPGSSFLELSQLAGHE- 126
           ME  +  L   + +   GGG+  + +   + KL  RER+  LLD GS F E+  L  H  
Sbjct: 1   MESKIKNLNEKLAQAYLGGGQARIDKQHEKKKLTARERVMYLLDEGS-FEEIGALVTHRT 59

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

Query: 183 LPCIYLVDSGGAYLPKQAEVFPDKENFGRVFYNESVMSSDGIPQIAIVLGSCTAGGAYIP 242
            P I L DSGGA + +          +  +FY ++V SS  IPQI+ ++G C  G  Y P
Sbjct: 120 APIIGLNDSGGARIQEGVRSLG---GYADIFY-KNVQSSGVIPQISAIMGPCAGGAVYSP 175

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

Query: 303 AIGRNIVKNLHMAAKQGMEGTFGSKNLVYKEPLYDINELRSIAPVDHKQQFDVRSIIARI 362
                 VK L     Q    T        K+ + +   L +I P +  Q +D+ S+IA I
Sbjct: 236 ----EDVKKLLSYLPQNNTETPTLLPFKLKDEVRE--SLSTIIPANANQPYDMHSVIAGI 289

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

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

Query: 478 GRAYSPDFMFIWPNARIGIMGGAQAAGVLTQIERATKKRQGIKWTEEEEEAFKKKTVDAY 537
            +    D  F WP+A I +MG   AA ++ + E      + +KW E+E E          
Sbjct: 410 SKHIGSDMNFAWPSAEIAVMGAKGAAEIIFKKEINAADDKEVKWKEKEAE--------YA 461

Query: 538 EREANPYYSTARLWDDGVIDPCDTRKVLGLCLSAALNRPLE 578
           E  ANPY +  R + D VI P DTR+ L    +   N+ +E
Sbjct: 462 ELFANPYSAAERGFIDEVILPKDTRRKLIKAFAMLENKEVE 502


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: 770
Number of extensions: 36
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: 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 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