GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Dinoroseobacter shibae DFL-12

Align Formate-dependent phosphoribosylglycinamide formyltransferase; 5'-phosphoribosylglycinamide transformylase 2; Formate-dependent GAR transformylase; GAR transformylase 2; GART 2; Non-folate glycinamide ribonucleotide transformylase; Phosphoribosylglycinamide formyltransferase 2; EC 2.1.2.- (characterized)
to candidate 3607265 Dshi_0680 phosphoribosylaminoimidazole carboxylase, ATPase subunit (RefSeq)

Query= SwissProt::P33221
         (392 letters)



>FitnessBrowser__Dino:3607265
          Length = 357

 Score =  113 bits (282), Expect = 1e-29
 Identities = 109/363 (30%), Positives = 167/363 (46%), Gaps = 20/363 (5%)

Query: 8   LRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDAL 67
           L P A  + +LG G+LG+ +++   RLG      +  A  PA  VA         D DAL
Sbjct: 5   LAPGAV-IGMLGGGQLGRMLSMAAARLGFRCHIFEPGAAPPAGQVAEAVTTAGYDDLDAL 63

Query: 68  RRVVELEKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQL 127
           RR  E+     I  E E I T  L  LE     + P  RA  ++ +R   +      L L
Sbjct: 64  RRFAEVVD--VITYEFENIPTAALDVLEALR-PIHPGRRALAVSQDRLTEKEFL-RGLGL 119

Query: 128 PTSTYRFADSESLFREAVADIGYPCIVKPV-MSSSGKGQTFIRSAEQLAQAWKYAQQGGR 186
            T+ +   D  +    A+A IG P I+K   +   GKGQT + +    A+A         
Sbjct: 120 QTAPFAPVDDAAGLEAALAAIGTPAILKTRRLGYDGKGQTRLTAPGDAAEAL-----AAM 174

Query: 187 AGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHR-QEDGDYRESWQPQQMSPLALE 245
           AGA   I+EG V+F  E++++     DG   C   G     DG    +  P ++S     
Sbjct: 175 AGAP-AILEGFVEFSHEVSVIAARGQDGAVACFDPGENVHRDGILATTTVPARLSHAQRT 233

Query: 246 RAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVR 305
            A  +A +++ AL   G+ GVELFV    +I +E++PR H++G  T     + +F  H+R
Sbjct: 234 DAVLLAGRILNALDYVGVMGVELFVTRGGLIVNEIAPRVHNSGHWTQTGCVIDQFEQHIR 293

Query: 306 AFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNV-QNAVGADLQIRLFGKPEIDGSRRL 364
           A  G P+G     G   + V++  L   ++  D V + A   D+ + L+GK E    R++
Sbjct: 294 AVAGWPLGD----GQRHADVVMENLIGSDM--DRVPELAAARDVALHLYGKAETRAGRKM 347

Query: 365 GVA 367
           G A
Sbjct: 348 GHA 350


Lambda     K      H
   0.320    0.136    0.390 

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: 292
Number of extensions: 18
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: 392
Length of database: 357
Length adjustment: 30
Effective length of query: 362
Effective length of database: 327
Effective search space:   118374
Effective search space used:   118374
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: 50 (23.9 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