GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gbuA in Phaeobacter inhibens BS107

Align guanidinobutyrase subunit (EC 3.5.3.7) (characterized)
to candidate GFF30 PGA1_c00300 guanidinobutyrase

Query= metacyc::MONOMER-11557
         (320 letters)



>FitnessBrowser__Phaeo:GFF30
          Length = 326

 Score =  134 bits (337), Expect = 3e-36
 Identities = 93/304 (30%), Positives = 152/304 (50%), Gaps = 13/304 (4%)

Query: 23  GIATMLRLPHLQSAKGLDAAFIGVPLDIGT-SLRSGTRFGPRQIRAESVMIRPYNMATGA 81
           GI T+ R P+L    G D A +GVP   G  +       GPR +R  S + R  +     
Sbjct: 17  GIPTLFRCPNLP-VDGQDIALVGVPHSAGNGTTERDQHLGPRALRNVSSVQRRMHSGFQL 75

Query: 82  APFDSLSVADIGDVAINTFN-LLDAVRIIEEAYDEIVEHNVIPMTLGGDHTITLPILRAL 140
            P+++  + D+GDV     N   D ++ I   Y +I +    P+++GGDH+IT  I++AL
Sbjct: 76  DPWNAAKIVDLGDVPFPKANDNEDCIQQITNFYQQIDKAGARPVSVGGDHSITGGIVQAL 135

Query: 141 H----KKHGKIGLVHIDAHADVN---DHMFGEKIAHGTTFRRAVEEGLLDCDRVVQIGLR 193
                 K   I  +H+DAH DV    DH  G K +         ++G +D    +QIG+R
Sbjct: 136 GCGAITKGEPICFLHLDAHTDVFTKVDHFLGAKKSAAHWGAYLADQGKVDPAHSMQIGIR 195

Query: 194 AQGYTADDFNWSRRQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVYLSFDIDGIDPAWA 253
               T D    S   G+ VV  ++   + L  ++A+V E + G PVY++FD+D +DP  A
Sbjct: 196 GHARTLDWLQPSYEYGYNVVTMKDYRRRGLADVVAQVTEVLAGRPVYITFDLDCLDPTIA 255

Query: 254 PGTGTPEIG--GLTTIQAMEIIRGCHGLDLIGCDLVEVSPPYDTTGN-TSLLGANLLFEM 310
           PG    E G  G     A+ ++    G++++G D+V + P  D+    T+L    ++FE+
Sbjct: 256 PGVSNIEAGEKGFGIDDAVGLLHAVRGMNIVGGDVVCMMPTKDSPNQITALTAGAIMFEI 315

Query: 311 LCVL 314
           + ++
Sbjct: 316 ISMI 319


Lambda     K      H
   0.322    0.141    0.431 

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: 263
Number of extensions: 12
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: 320
Length of database: 326
Length adjustment: 28
Effective length of query: 292
Effective length of database: 298
Effective search space:    87016
Effective search space used:    87016
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: 48 (23.1 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