GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Acidovorax sp. GW101-3H11

Align propionyl-CoA carboxylase β subunit (EC 6.4.1.3) (characterized)
to candidate Ac3H11_4479 Biotin carboxylase (EC 6.3.4.14)

Query= metacyc::MONOMER-17284
         (514 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4479
          Length = 1095

 Score =  212 bits (540), Expect = 5e-59
 Identities = 157/512 (30%), Positives = 241/512 (47%), Gaps = 32/512 (6%)

Query: 4    PEEQLATLFRLRER---ALQGGGPERVAQQHARGKLTARERLALLLDPNSFQEIGALASS 60
            P+   A L R+ +R         PE +A++HA+G  TARE +A L D  SF E GALA +
Sbjct: 579  PDHIRADLQRVIDRHAFTFDAARPEAIAKRHAQGGRTARENIADLCDNGSFIEYGALAIA 638

Query: 61   PLG------DEDQRVPGDGIVTGFGKINGR-------RVAVFAQDFTVMGGSFSAVQANK 107
                     D     P DG+VTG G ING        R  V + D TV+ G+  A    K
Sbjct: 639  AQARRRSKEDLIANTPADGMVTGIGGINGALFGDEKSRAVVMSYDATVLAGTQGARNHAK 698

Query: 108  ICRMQDLAIESGIPIIGLNDSGGARIQEGVRSLAA--YGEVFVRNVMASGVVPQISAILG 165
              RM  +A+   +P++   + GG R  +    + A  +   F      SG VP I    G
Sbjct: 699  TDRMLGIALAQKLPVVLFAEGGGGRPGDTDMPIVAGLHVHTFASYAALSGQVPVIGIAAG 758

Query: 166  PCAGGAVYSPALTDFVIMSESTGYMFLTGPDVIKAVSGRELSTQELGGAAVHCVRSGVAH 225
             C  G       +D +I +  +  + + GP +I+         +++G + V    +GV  
Sbjct: 759  RCFAGNAALLGCSDVIIATRGSN-IGMGGPAMIEGGGLGVFKPEQIGPSRVQHA-NGVID 816

Query: 226  LSAADDRAVIELIKRLLSYLPQNNNEDPPQIMPYDRADRIEPALNSLVPADERQGYDIHT 285
            +   D+   ++  +  LS+        P    P  R       L ++VP +  + YD  T
Sbjct: 817  VLVDDEAGAVQAARHYLSFF---QGRTPEWSAPDQRL------LRAVVPENRLRVYDTRT 867

Query: 286  LINLICDYDSFLEIQPLFAPNAVVGFARLDGYAVGIVANQPAVMAGALDIDASDKIARFV 345
             +  + D  S L ++  F        AR++G  VG++AN P  + GA+D DA+DK ARF+
Sbjct: 868  AMAGLVDDASLLPLRTGFGAGIHTALARIEGRPVGLLANNPQHLGGAIDADAADKGARFM 927

Query: 346  RICDAFNIPLITFVDTPGFLPGVEQEYGGVIRHGAKIIYAYSEATVPKISVVVRKAIGGA 405
            ++C+A  +P+++ VDTPGF+ G E E    +RH +++    +   VP  SVV+RK  G  
Sbjct: 928  QLCNAHGLPIVSLVDTPGFMVGPEVEATAQVRHVSRLFVTAASLRVPTFSVVLRKGYGLG 987

Query: 406  YVAMSSKQLRCDL-NFAWPSAQIAVMGAEGAVRILRREELRTAENPAQLMEQFIADYRRR 464
             + M++      +   AWP+ +   MG EGAVR+  R+EL      A+    F     + 
Sbjct: 988  AMGMTAGGFHAPVFTVAWPTGEFGAMGLEGAVRLGFRKELEALPEGAERDALFAKLLAKS 1047

Query: 465  YFN--PYHAADLGQIDEVIEPAETRPRLIRAL 494
            Y N    H A   +ID VI+PA+TR  L R L
Sbjct: 1048 YANGEAMHMAATLEIDAVIDPADTRAWLARGL 1079


Lambda     K      H
   0.321    0.138    0.400 

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: 1402
Number of extensions: 64
Number of successful extensions: 8
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: 514
Length of database: 1095
Length adjustment: 40
Effective length of query: 474
Effective length of database: 1055
Effective search space:   500070
Effective search space used:   500070
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: 55 (25.8 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