GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS16635
          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:

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