GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccA1 in Phaeobacter inhibens BS107

Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate GFF1016 PGA1_c10330 methylcrotonoyl-CoA carboxylase subunit alpha

Query= metacyc::MONOMER-13597
         (509 letters)



>lcl|FitnessBrowser__Phaeo:GFF1016 PGA1_c10330 methylcrotonoyl-CoA
           carboxylase subunit alpha
          Length = 645

 Score =  340 bits (873), Expect = 7e-98
 Identities = 193/450 (42%), Positives = 274/450 (60%), Gaps = 11/450 (2%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           F ++L+ANRGEIA RV++  + MG+  +AVYS+AD  A H + ADEA +IG +   DSYL
Sbjct: 2   FDKILIANRGEIACRVMETARAMGVRTVAVYSDADVTAKHVQMADEAVHIGGSAPADSYL 61

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
             + II  A+++   AIHPGYGFLSEN  F +AVE AG++FIGPS++ +RK+  K   K 
Sbjct: 62  KGDVIIRVAQESGAQAIHPGYGFLSENPAFVDAVEAAGLSFIGPSADAIRKMGLKDAAKA 121

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183
           L   AGVP  PG  G     +     AEKIGYP+++KA +GGGG G+  V+   +  D  
Sbjct: 122 LMEKAGVPVVPGYHGANQDAEFLAGEAEKIGYPVLIKAVAGGGGKGMRLVEAPAEFSDAL 181

Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVV-AWERECTIQRRNQKLIE 242
           +  +  A  AFG  D+ IEKY   PRHIE Q+ GD  G + V  +ER+C++QRR+QK+IE
Sbjct: 182 KSAQGEATTAFGNPDVLIEKYIQQPRHIEVQVFGD--GTHAVHLFERDCSLQRRHQKVIE 239

Query: 243 EAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAF--SDVSR--DFYFLELNKRLQV 298
           EAP+P +  E RE+M E  ++  + I Y   GT E     SD  R   F+F+E+N RLQV
Sbjct: 240 EAPAPGMTAEMREAMGEAGVRAAEAIGYKGAGTVEFIVDGSDGLRTDGFWFMEMNTRLQV 299

Query: 299 EHPTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSG 358
           EHP TELI  +DLV+ Q+++A+GE LP  Q+DL   + G A E R+ AED    F  ++G
Sbjct: 300 EHPVTELITGVDLVEWQLRVASGESLPAQQDDLT--ITGHAFEARLYAEDVPKGFLPATG 357

Query: 359 FVTYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIG 418
            +T+   P     R DSG+ +G  + P+YD ++SK+IV+G +R  A+    RAL   ++ 
Sbjct: 358 TLTHLSFPA--ECRADSGVRAGDTISPWYDPMISKVIVHGATRSVALSKLRRALERTEVA 415

Query: 419 GIKTTIELYKWIMQDPDFQEGKFSTSYISQ 448
           G  T +     +     F  G+  T  I++
Sbjct: 416 GTVTNLAFLGALASHQGFGRGEVDTGLIAR 445


Lambda     K      H
   0.317    0.135    0.385 

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: 738
Number of extensions: 40
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: 509
Length of database: 645
Length adjustment: 36
Effective length of query: 473
Effective length of database: 609
Effective search space:   288057
Effective search space used:   288057
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 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 paper from 2022 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