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 α subunit (EC 6.4.1.3) (characterized)
to candidate CA265_RS10640 CA265_RS10640 methylcrotonoyl-CoA carboxylase

Query= metacyc::MONOMER-17283
         (535 letters)



>FitnessBrowser__Pedo557:CA265_RS10640
          Length = 542

 Score =  545 bits (1405), Expect = e-159
 Identities = 267/528 (50%), Positives = 372/528 (70%), Gaps = 16/528 (3%)

Query: 14  DFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRIDTLIDPDSSFLEI 73
           +F  N   ++ L  +L+ RL +I  GGG +   + +E+GKL  R+RI  LID DS+FLE+
Sbjct: 4   EFNKNEDVNKQLVYELKTRLKKIYLGGGEKNAAKQKEKGKLLARERIAYLIDKDSNFLEV 63

Query: 74  GALAAYNVYDEE--VPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPLTVKKHLRAQEI 131
           GA  A  +Y E+   P+AG+VCGIG V+GR  MI+ANDATVK G +FP+T KK+LRAQEI
Sbjct: 64  GAFTADGMYAEQGGCPSAGVVCGIGYVSGRQCMIVANDATVKAGAWFPMTAKKNLRAQEI 123

Query: 132 ARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQIACVMGSCTAG 191
           A ENRLP IYLVDS G YLP+Q E+FPD++HFGR+F N A MS+EGI QI+ +MG+C AG
Sbjct: 124 AMENRLPVIYLVDSAGVYLPMQDEIFPDKEHFGRMFRNNAIMSSEGIVQISAIMGACVAG 183

Query: 192 GAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTRISGVADYFAND 251
           GAY+P MSDE +IV   G++FL G  LVK+A GEEV  E LGGA  H  ISGV DY   +
Sbjct: 184 GAYLPIMSDEAMIVDKTGSVFLAGSYLVKSAIGEEVDNETLGGATTHCEISGVTDYKHLN 243

Query: 252 DREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQSYDVREVIARIV 311
           D+  L  +R+I++ LG  Q A ++   P  P+    E+YGILP +  + Y++ ++I R+V
Sbjct: 244 DQACLDSIRNIMSMLGAPQNAGFDRIKPAKPKEKEEELYGILPENRDKPYEIMDIINRLV 303

Query: 312 DGSRLHEFKTRYGTTLVCGFAHIEGFPVGILAN--------------NGILFSESALKGA 357
           DGS   E+K  YG ++VCG   I+G+ VGI+AN               G+++S+SA K  
Sbjct: 304 DGSEFEEYKKGYGQSIVCGLGRIDGWAVGIVANQRKVVKSKKGEMQFGGVIYSDSADKAT 363

Query: 358 HFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSF 417
            FI  C  + IPLVFLQ++TGFMVG + E+GGI KDGAK+V AV+ + VPKFT+++G S+
Sbjct: 364 RFIMNCNQKKIPLVFLQDVTGFMVGSRSEHGGIIKDGAKMVNAVANSVVPKFTIVLGNSY 423

Query: 418 GAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERF 477
           GAGNY MCG+AY PR ++ WP A+I+VMGG+QAA  LL I+  +L+A+G+ +TPE++   
Sbjct: 424 GAGNYAMCGKAYDPRLIYAWPTAKIAVMGGSQAAKTLLQIQEASLKAKGEVITPEKEAEL 483

Query: 478 MAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPV 525
           +  I  +Y+ +  PYYA++RLW DG+IDP+ETR+V+++G+ AA ++P+
Sbjct: 484 LKEITDRYDSQTTPYYAASRLWVDGIIDPLETRKVISMGIEAANQSPI 531


Lambda     K      H
   0.322    0.139    0.423 

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: 767
Number of extensions: 30
Number of successful extensions: 5
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: 535
Length of database: 542
Length adjustment: 35
Effective length of query: 500
Effective length of database: 507
Effective search space:   253500
Effective search space used:   253500
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 (21.9 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