GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccB in Pedobacter sp. GW460-11-11-14-LB5

Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate CA265_RS16635 CA265_RS16635 methylmalonyl-CoA carboxyltransferase

Query= SwissProt::Q3J4E3
         (510 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS16635 CA265_RS16635
           methylmalonyl-CoA carboxyltransferase
          Length = 513

 Score =  643 bits (1659), Expect = 0.0
 Identities = 316/500 (63%), Positives = 390/500 (78%), Gaps = 5/500 (1%)

Query: 15  ARAGGGQRRVEAQHKRGKLTARERIELLLDEGSFEEFDMFVRHRCTDFGMQDDRPAGDGV 74
           A  GGGQ R+++QHK+GKLTARERI  L+DEGSFEE  M V HR TDFGM+ ++  GDGV
Sbjct: 15  ANLGGGQARIDSQHKKGKLTARERIHFLMDEGSFEEIGMMVTHRSTDFGMEREKYLGDGV 74

Query: 75  VTGWGTINGRMVYVFSQDFTVFGGSLSETHAQKICKIMDMAMQNGAPVIGLNDSGGARIQ 134
           VTG+GT++GR+ YVFSQDFTVFGGSLSETHA+KICK+MDMAM+NGAP+IGLNDSGGARIQ
Sbjct: 75  VTGYGTVSGRLTYVFSQDFTVFGGSLSETHAEKICKLMDMAMKNGAPLIGLNDSGGARIQ 134

Query: 135 EGVASLAGYADVFQRNIMASGVIPQISVIMGPCAGGAVYSPAMTDFIFMVRDTSYMFVTG 194
           EGV SL GYAD+F +N+ ASGVIPQ+S IMGPCAGGAVYSPA+TDFI MV +TSYMFVTG
Sbjct: 135 EGVVSLGGYADIFYKNVQASGVIPQLSAIMGPCAGGAVYSPAITDFILMVENTSYMFVTG 194

Query: 195 PDVVKTVTNEVVTAEELGGASTHTKKSSVADGAFENDVEALYEIRRLVDFLPLSNRTPAP 254
           P+VVKTVT+E VT+EELGGASTH  KS V   A  N++EA+  +++L+ ++P +    A 
Sbjct: 195 PNVVKTVTHEEVTSEELGGASTHATKSGVTHFACANEIEAINHLKKLLSYMPQNCEEIAD 254

Query: 255 VRPFFDDVARIEDSLDTLIPDNPNQPYDMKELILKIADEADFYEIQKDFAANIITGFIRL 314
             P ++        L+T +P+N +QPYD++E+I  +AD   F E+   +A NI+ GF RL
Sbjct: 255 HLP-YETADESRPELNTFMPENASQPYDIREVISAVADTDSFLEVHAAYAENIVVGFARL 313

Query: 315 EGQTVGVVANQPMVLAGCLDIDSSRKAARFVRFCDAFNIPILTLVDVPGFLPGTGQEYGG 374
            G+++G+VANQP  LAG LD +SS KAARFVRFCD FNIP+L   DVPGFLPGT QE+ G
Sbjct: 314 AGRSIGIVANQPAYLAGVLDSNSSTKAARFVRFCDCFNIPLLVFEDVPGFLPGTDQEWNG 373

Query: 375 VIKHGAKLLFAYGEATVPKVTVITRKAYGGAYDVMASKHLRGDFNYAWPTAEIAVMGAKG 434
           +I +GAKLL+A+ EATVP++TVITRKAYGGAYDVM SKH+  D NYAWP+AEIAVMGAKG
Sbjct: 374 IITNGAKLLYAFSEATVPRITVITRKAYGGAYDVMNSKHIGADMNYAWPSAEIAVMGAKG 433

Query: 435 ATEILYRSELGD----KEKIAARAKEYEDRFANPFVAAERGFIDEVIMPHSTRRRVSKAF 490
           A EI+++ E+      +EK   + K Y D FANP+ AAERGF+DEVI P  TR ++ KAF
Sbjct: 434 AAEIIFKREITSAEKPEEKWLEKEKLYSDIFANPYRAAERGFVDEVIEPAQTRIKLIKAF 493

Query: 491 ASLRNKKLANPWKKHDNIPL 510
             L NK + NP KKH NIPL
Sbjct: 494 KMLENKVVNNPRKKHGNIPL 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: 785
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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