GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Caulobacter crescentus NA1000

Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate CCNA_02054 CCNA_02054 methylmalonyl-CoA carboxylase, carboxyltransferase subunit

Query= SwissProt::Q3J4E3
         (510 letters)



>FitnessBrowser__Caulo:CCNA_02054
          Length = 510

 Score =  805 bits (2078), Expect = 0.0
 Identities = 392/510 (76%), Positives = 443/510 (86%)

Query: 1   MKDILQELENRRAIARAGGGQRRVEAQHKRGKLTARERIELLLDEGSFEEFDMFVRHRCT 60
           M+ IL+ELE RR  A+AGGG+ RV +QH +GKLTARERIELLLDEGSFEEFDMFV HRC 
Sbjct: 1   MQHILEELERRRQQAKAGGGETRVASQHAKGKLTARERIELLLDEGSFEEFDMFVEHRCA 60

Query: 61  DFGMQDDRPAGDGVVTGWGTINGRMVYVFSQDFTVFGGSLSETHAQKICKIMDMAMQNGA 120
           DFGMQD +  GDGVVTGWGTING++VYVFS+DFTVFGGSLS  HAQKI K+   AM+ GA
Sbjct: 61  DFGMQDQKIPGDGVVTGWGTINGKVVYVFSKDFTVFGGSLSNAHAQKIVKVQRQAMKVGA 120

Query: 121 PVIGLNDSGGARIQEGVASLAGYADVFQRNIMASGVIPQISVIMGPCAGGAVYSPAMTDF 180
           PVIGL D+GGARIQEGV SLAGYAD+F  N+MASGVIPQISVIMGPCAGG VYSPAMTDF
Sbjct: 121 PVIGLFDAGGARIQEGVDSLAGYADIFVENVMASGVIPQISVIMGPCAGGDVYSPAMTDF 180

Query: 181 IFMVRDTSYMFVTGPDVVKTVTNEVVTAEELGGASTHTKKSSVADGAFENDVEALYEIRR 240
           IFMV+DTSYMFVTGPDVVKTVTNEVVTAEELGGA  H  KS VA+GAFEND+EA+ ++RR
Sbjct: 181 IFMVKDTSYMFVTGPDVVKTVTNEVVTAEELGGARVHAAKSGVAEGAFENDLEAMTQVRR 240

Query: 241 LVDFLPLSNRTPAPVRPFFDDVARIEDSLDTLIPDNPNQPYDMKELILKIADEADFYEIQ 300
           L+DFLP SNR PAP R  FD+  R E SLDTL+P +P +PYDMKELILK+ DEADF+EI 
Sbjct: 241 LIDFLPSSNREPAPERESFDEPLRDEMSLDTLVPADPTKPYDMKELILKVVDEADFFEIS 300

Query: 301 KDFAANIITGFIRLEGQTVGVVANQPMVLAGCLDIDSSRKAARFVRFCDAFNIPILTLVD 360
            ++A NII GF R++G+TVG+VANQP VLAG LDIDSSRKAARFVRFCDAFNIPI+T VD
Sbjct: 301 SEWAKNIICGFARMDGETVGIVANQPQVLAGVLDIDSSRKAARFVRFCDAFNIPIVTFVD 360

Query: 361 VPGFLPGTGQEYGGVIKHGAKLLFAYGEATVPKVTVITRKAYGGAYDVMASKHLRGDFNY 420
           VPGF+PGT QEYGG+IKHGAKLLFAY EATVPK+TVITRKAYGGAYDVM+SKHLRGD NY
Sbjct: 361 VPGFMPGTKQEYGGLIKHGAKLLFAYTEATVPKITVITRKAYGGAYDVMSSKHLRGDLNY 420

Query: 421 AWPTAEIAVMGAKGATEILYRSELGDKEKIAARAKEYEDRFANPFVAAERGFIDEVIMPH 480
           AWPTAEIAVMGAKGA EI++R E  D E +AAR  EY+DRFANPFVAA+RG+ID+VIMPH
Sbjct: 421 AWPTAEIAVMGAKGAVEIIFRQEAKDPEALAAREAEYKDRFANPFVAAQRGYIDDVIMPH 480

Query: 481 STRRRVSKAFASLRNKKLANPWKKHDNIPL 510
            TRRR+ +   SL+ K+L+NPWKKHDNIPL
Sbjct: 481 GTRRRIVRGLKSLKGKELSNPWKKHDNIPL 510


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: 856
Number of extensions: 30
Number of successful extensions: 1
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: 510
Length adjustment: 34
Effective length of query: 476
Effective length of database: 476
Effective search space:   226576
Effective search space used:   226576
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