GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccB in Bacteroides thetaiotaomicron VPI-5482

Align Propionyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.3) (characterized)
to candidate 350978 BT1450 propionyl-CoA carboxylase beta chain (NCBI ptt file)

Query= reanno::PS:Dsui_0517
         (510 letters)



>lcl|FitnessBrowser__Btheta:350978 BT1450 propionyl-CoA carboxylase
           beta chain (NCBI ptt file)
          Length = 514

 Score =  676 bits (1745), Expect = 0.0
 Identities = 333/514 (64%), Positives = 407/514 (79%), Gaps = 4/514 (0%)

Query: 1   MHDIIHELEKKREAARLGGGQKRIDSQHKKGKLTARERLELLLDPDSFEEWDMFKEHRCT 60
           M ++I  LE+    A  GGG  RI+ QH  GKLTARER++LLL+  SF E D    HRCT
Sbjct: 1   MKELIKNLEELNRKAEKGGGDARIEKQHSVGKLTARERIDLLLEKGSFIELDKLVTHRCT 60

Query: 61  DFGMAETKNPGDGVVTGYGTINGRLVFVFSQDFTVFGGSLSETHAEKICKVMDHAMKVGA 120
           DFGM + K  GDGVVTGYG I  RLV+VF+QDFTVFGG+LSETHA+KICKVMD AM++GA
Sbjct: 61  DFGMEKQKFSGDGVVTGYGMIGKRLVYVFAQDFTVFGGALSETHAKKICKVMDMAMQMGA 120

Query: 121 PVIGLNDSGGARIQEGVASLGGYADVFQRNVMASGVIPQISMIMGPCAGGAVYSPAMTDF 180
           P+IGLNDSGGARIQEGV SL GYA++F RN MASGVIPQIS IMGPCAGGAVYSPA+TDF
Sbjct: 121 PIIGLNDSGGARIQEGVRSLAGYAEIFLRNSMASGVIPQISAIMGPCAGGAVYSPALTDF 180

Query: 181 IFMVKDSSYMFVTGPEVVKTVTHEEVTAEELGGAVTHTTKSGVADLAFENDVEALNYLRR 240
           I MVK+S YMF+TGP+VVK+VT EEV+ E+LGG   H TKSGVA L+ END+E +NY+R 
Sbjct: 181 ILMVKNSGYMFITGPDVVKSVTQEEVSKEDLGGVGIHMTKSGVAHLSAENDIECINYIRE 240

Query: 241 LVNFLPANNREKPPVQKTNDPAERLDFSLDTLVPDNANKPYDMKELIIKMVDDCDFFEIQ 300
           L+++LP NN E+PP   TND   RL   L  LVP N N+PY++KE+I  + DD +FFE+Q
Sbjct: 241 LISYLPGNNMEEPPFVVTNDSPTRLTPELSDLVPTNPNQPYNIKEMIEAVADDNNFFELQ 300

Query: 301 PDYAKNIITGFARMDGHPVGIVANQPLVLAGCLDIKSSIKAARFVRFCDAFNIPVVTLVD 360
            ++A NI+TG+ R++G  +G+VANQPLVLAG LDI +SIKAARFVRFCDAFNIP++TLVD
Sbjct: 301 AEFAANIVTGYIRLNGKTIGVVANQPLVLAGTLDINASIKAARFVRFCDAFNIPLLTLVD 360

Query: 361 VPGFMPGTSQEYGGIIKHGAKLLYAYAECTVPKVTLITRKAYGGAYDVMSSKHLRGDVNL 420
           VPGF+PG  QEYGGII++GAKLLYAY E TVPKVT+ITRKAYGGAYDVMSSKH+RGDVNL
Sbjct: 361 VPGFLPGVDQEYGGIIRNGAKLLYAYCEATVPKVTVITRKAYGGAYDVMSSKHIRGDVNL 420

Query: 421 AWPSAEIAVMGPKGAVEIIFREE----KNDPAKLAEREAEYKAKFANPFVAGARGFIDDV 476
           A+P+AEIAVMGP GAV I+F++E    +    +  E +++Y+ KFANP+ A   G++D+V
Sbjct: 421 AFPTAEIAVMGPDGAVNILFKKEIEKSQTPEERRKELQSDYREKFANPYRAAELGYVDEV 480

Query: 477 IMPNETRKRICRSLAMLRDKKLDNPWRKHGNIPL 510
           I P  TR R+ RS  ML +K+  NP +KH NIPL
Sbjct: 481 IDPAVTRLRLIRSFEMLANKRQSNPPKKHSNIPL 514


Lambda     K      H
   0.320    0.137    0.409 

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: 817
Number of extensions: 26
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: 514
Length adjustment: 35
Effective length of query: 475
Effective length of database: 479
Effective search space:   227525
Effective search space used:   227525
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