GapMind for catabolism of small carbon sources

 

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

Align glycolate oxidase subunit glcD (characterized)
to candidate 3608683 Dshi_2076 FAD linked oxidase domain protein (RefSeq)

Query= CharProtDB::CH_024646
         (499 letters)



>FitnessBrowser__Dino:3608683
          Length = 472

 Score =  141 bits (355), Expect = 6e-38
 Identities = 133/436 (30%), Positives = 199/436 (45%), Gaps = 37/436 (8%)

Query: 58  LVVLPKQMEQVTAILAVCHRLRVPVVTRGAGTGLSGGAL----PLEKGVLLVMARFKEIL 113
           L+V P   E+V  ++ +    +VP++  G GTGL GG +    P+   V+L + R + I 
Sbjct: 43  LLVAPGATEEVATLVRLAQAHKVPIIPYGGGTGLVGGQIAPAGPVP--VILSLRRMRSIR 100

Query: 114 DINPVGRRARVQPGVRNLAISQAVAPHNLYYAPDPSSQIACSIGGNVAENAGGVHCLKYG 173
            + P         G     + QA       +    +S+ + +IGG +A NAGGV+ L+YG
Sbjct: 101 AVYPEENVLVADAGAVLAEVQQAARDVGRLFPLSLASEGSATIGGVLATNAGGVNVLRYG 160

Query: 174 LTVHNLLKIEVQTLDGEALTLGSDAL--DSPGFDLLALFTGSEGMLGVTTEVTVKLLPKP 231
                 L +E    DG A+  G   L  ++ G+DL  L  G+EG LG+ T   ++L P P
Sbjct: 161 NARDLCLGLEAVMPDG-AIWHGLTRLRKNNMGYDLRHLLIGAEGTLGIITGAALRLSPLP 219

Query: 232 PVARVLL-------ASFDSVEKAGLAVGDII-ANGIIPG-GLEMMDNL--SIRAAEDFIH 280
               V L       A+ D +  AG   GD I A  +I G G E        +RA  D   
Sbjct: 220 QRHGVGLLVVDSPAAALDLLALAGEVAGDTISAFELISGRGFEFFAETMPEMRAPLD--- 276

Query: 281 AGYPVDAEAILLCELDGVESDVQEDCERVNDILLKAG-ATDVRLAQDEAERVRFWAGRKN 339
              PV A ++L+        D +   E +     +AG  +D  +AQ EA+    WA R+N
Sbjct: 277 ---PVPAWSVLIDLAGASGFDPEGALETLFARAAEAGLVSDGVIAQSEAQADALWALREN 333

Query: 340 AFPAVGRISPDYYCMDGTIPRRALPGVLE-GIARLSQQYDLRVANVFHAGDGNMHPLILF 398
             P   R        D ++P   +P  +E   ARL+   D R+    H GDGN+H  +  
Sbjct: 334 -IPEANRRIGSVSSHDISVPLSEIPNFIETATARLAGIGDYRINCFGHVGDGNLHYNVF- 391

Query: 399 DANEPGEFARAEELGGKILELCV-----EVGGSISGEHGIGREKINQMCAQFNSDEITTF 453
              +PG      E     ++ CV     E+GGS+S EHG+GR K+  +    +  +    
Sbjct: 392 --PQPGRSRADHEDERPAIKTCVHDLVHELGGSVSAEHGVGRLKVEDLERYGDPVKQAAM 449

Query: 454 HAVKAAFDPDGLLNPG 469
            A+K A DP GL+NPG
Sbjct: 450 RAIKDALDPHGLMNPG 465


Lambda     K      H
   0.320    0.140    0.415 

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: 659
Number of extensions: 39
Number of successful extensions: 6
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: 499
Length of database: 472
Length adjustment: 34
Effective length of query: 465
Effective length of database: 438
Effective search space:   203670
Effective search space used:   203670
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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