GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF1016
          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:

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