GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Lacinutrix algicola AKS293

Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate WP_055436809.1 ASC41_RS11575 acyl-CoA carboxylase subunit beta

Query= SwissProt::Q3J4E3
         (510 letters)



>NCBI__GCF_001418085.1:WP_055436809.1
          Length = 513

 Score =  669 bits (1725), Expect = 0.0
 Identities = 331/514 (64%), Positives = 403/514 (78%), Gaps = 5/514 (0%)

Query: 1   MKDILQELENRRAIARAGGGQRRVEAQHKRGKLTARERIELLLDEGSFEEFDMFVRHRCT 60
           M+  ++ L  + A A  GGGQ R++ QH++ KLTARER+  LLDEGSFEE    V HR  
Sbjct: 1   MESKIKNLNEKLAQAYLGGGQARIDKQHEKKKLTARERVMYLLDEGSFEEIGALVTHRTK 60

Query: 61  DFGMQDDRPAGDGVVTGWGTINGRMVYVFSQDFTVFGGSLSETHAQKICKIMDMAMQNGA 120
           DFGM   +  GDGVVTG+GT+NGR++YVF+QDFTVFGGSLSETHA+KICK+MD+A++ GA
Sbjct: 61  DFGMDKQQFYGDGVVTGYGTVNGRLIYVFAQDFTVFGGSLSETHAEKICKVMDLALKVGA 120

Query: 121 PVIGLNDSGGARIQEGVASLAGYADVFQRNIMASGVIPQISVIMGPCAGGAVYSPAMTDF 180
           P+IGLNDSGGARIQEGV SL GYAD+F +N+ +SGVIPQIS IMGPCAGGAVYSPAMTDF
Sbjct: 121 PIIGLNDSGGARIQEGVRSLGGYADIFYKNVQSSGVIPQISAIMGPCAGGAVYSPAMTDF 180

Query: 181 IFMVRDTSYMFVTGPDVVKTVTNEVVTAEELGGASTHTKKSSVADGAFENDVEALYEIRR 240
             MV DTSYMFVTGP+VVKTVTNE VT+EELGGASTH+ KS VA     ND+E L ++++
Sbjct: 181 TIMVEDTSYMFVTGPNVVKTVTNEEVTSEELGGASTHSTKSGVAHKTSSNDIECLEDVKK 240

Query: 241 LVDFLPLSNRTPAPVRPFFDDVARIEDSLDTLIPDNPNQPYDMKELILKIADEADFYEIQ 300
           L+ +LP  N T  P    F     + +SL T+IP N NQPYDM  +I  I DE  FYEI 
Sbjct: 241 LLSYLP-QNNTETPTLLPFKLKDEVRESLSTIIPANANQPYDMHSVIAGIIDEDSFYEIH 299

Query: 301 KDFAANIITGFIRLEGQTVGVVANQPMVLAGCLDIDSSRKAARFVRFCDAFNIPILTLVD 360
           K++A NI+ GF RL G+++G+VANQPM LAG LD++SS+KAARFVRFCDAFNIP+LTL D
Sbjct: 300 KNYAENILVGFARLGGRSIGIVANQPMYLAGVLDVNSSKKAARFVRFCDAFNIPLLTLED 359

Query: 361 VPGFLPGTGQEYGGVIKHGAKLLFAYGEATVPKVTVITRKAYGGAYDVMASKHLRGDFNY 420
           VPGFLPGT QE+ G+I HGAKLL+A+ EATVP++TVITRKAYGGAYDVM SKH+  D N+
Sbjct: 360 VPGFLPGTDQEWNGIIVHGAKLLYAFSEATVPRITVITRKAYGGAYDVMNSKHIGSDMNF 419

Query: 421 AWPTAEIAVMGAKGATEILYRSELG---DKE-KIAARAKEYEDRFANPFVAAERGFIDEV 476
           AWP+AEIAVMGAKGA EI+++ E+    DKE K   +  EY + FANP+ AAERGFIDEV
Sbjct: 420 AWPSAEIAVMGAKGAAEIIFKKEINAADDKEVKWKEKEAEYAELFANPYSAAERGFIDEV 479

Query: 477 IMPHSTRRRVSKAFASLRNKKLANPWKKHDNIPL 510
           I+P  TRR++ KAFA L NK++  P +KH NIPL
Sbjct: 480 ILPKDTRRKLIKAFAMLENKEVERPKRKHGNIPL 513


Lambda     K      H
   0.321    0.138    0.404 

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: 794
Number of extensions: 27
Number of successful extensions: 3
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: 510
Length of database: 513
Length adjustment: 35
Effective length of query: 475
Effective length of database: 478
Effective search space:   227050
Effective search space used:   227050
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.

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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