GapMind for catabolism of small carbon sources

 

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

Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate 351214 BT1686 propionyl-CoA carboxylase beta chain (NCBI ptt file)

Query= SwissProt::Q3J4E3
         (510 letters)



>FitnessBrowser__Btheta:351214
          Length = 517

 Score =  650 bits (1678), Expect = 0.0
 Identities = 326/510 (63%), Positives = 392/510 (76%), Gaps = 4/510 (0%)

Query: 5   LQELENRRAIARAGGGQRRVEAQHKRGKLTARERIELLLDEGSFEEFDMFVRHRCTDFGM 64
           ++EL  RRA+AR GGG++ +  QH++GK TARERI +LLDEGSFEE DMFV HRCT+FGM
Sbjct: 8   IKELIERRAVARIGGGEKAIAKQHEKGKYTARERIAMLLDEGSFEEMDMFVEHRCTNFGM 67

Query: 65  QDDRPAGDGVVTGWGTINGRMVYVFSQDFTVFGGSLSETHAQKICKIMDMAMQNGAPVIG 124
           +     GDGVVTG GTI GR+VY+F+QDFTV  GSLSET + KICKIMD AM+ GAP IG
Sbjct: 68  EKKHYPGDGVVTGCGTIEGRLVYLFAQDFTVTAGSLSETMSLKICKIMDQAMKMGAPCIG 127

Query: 125 LNDSGGARIQEGVASLAGYADVFQRNIMASGVIPQISVIMGPCAGGAVYSPAMTDFIFMV 184
           +NDSGGARIQEG+ +LAGYA++FQRNI+ASGVIPQIS I GPCAGGAVYSPA+TDF  M+
Sbjct: 128 INDSGGARIQEGINALAGYAEIFQRNILASGVIPQISGIFGPCAGGAVYSPALTDFTLMM 187

Query: 185 RDTSYMFVTGPDVVKTVTNEVVTAEELGGASTHTKKSSVADGAFENDVEALYEIRRLVDF 244
             TSYMF+TGP VVKTVT E V+ E LGGAS H+ KS V     + + E L  IR L+ +
Sbjct: 188 EGTSYMFLTGPKVVKTVTGEDVSQENLGGASVHSTKSGVTHFTAKTEEEGLALIRTLLSY 247

Query: 245 LPLSNRTPAPVRPFFDDVARIEDSLDTLIPDNPNQPYDMKELILKIADEADFYEIQKDFA 304
           +P +N   AP     D + R+EDSL+ +IPD+PN+PYDM E+I  I D  +F EIQKD+A
Sbjct: 248 IPQNNLEEAPYVDCTDPIDRLEDSLNDIIPDSPNKPYDMYEVISAIVDNGEFLEIQKDYA 307

Query: 305 ANIITGFIRLEGQTVGVVANQPMVLAGCLDIDSSRKAARFVRFCDAFNIPILTLVDVPGF 364
            NII GF R  GQ+VG+VANQP  LAG LD ++SRK ARFVRFCDAFNIPI++LVDVPGF
Sbjct: 308 KNIIIGFARFNGQSVGIVANQPKFLAGVLDSNASRKGARFVRFCDAFNIPIVSLVDVPGF 367

Query: 365 LPGTGQEYGGVIKHGAKLLFAYGEATVPKVTVITRKAYGGAYDVMASKHLRGDFNYAWPT 424
           LPGTGQEY GVI HGAKLL+AYGEATVPKVT+  RK+YGG++ VM+ K LRGD NYAWPT
Sbjct: 368 LPGTGQEYNGVILHGAKLLYAYGEATVPKVTITLRKSYGGSHIVMSCKQLRGDMNYAWPT 427

Query: 425 AEIAVMGAKGATEILYRSELGDKEK----IAARAKEYEDRFANPFVAAERGFIDEVIMPH 480
           AEIAVMG  GA E+LY  E  D+E     +A +  EY   FANP+ AA+ G+ID+VI P 
Sbjct: 428 AEIAVMGGAGAVEVLYAREAKDQENPAQFLAEKEAEYTKLFANPYNAAKYGYIDDVIEPR 487

Query: 481 STRRRVSKAFASLRNKKLANPWKKHDNIPL 510
           +TR RV +A   L+ KKL+NP KKH NIPL
Sbjct: 488 NTRFRVIRALQQLQTKKLSNPAKKHGNIPL 517


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: 756
Number of extensions: 23
Number of successful extensions: 4
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: 517
Length adjustment: 35
Effective length of query: 475
Effective length of database: 482
Effective search space:   228950
Effective search space used:   228950
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