GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcD in Synechococcus elongatus PCC 7942

Align glycolate oxidase subunit glcD (characterized)
to candidate Synpcc7942_0276 Synpcc7942_0276 glycolate oxidase subunit GlcD

Query= CharProtDB::CH_024646
         (499 letters)



>FitnessBrowser__SynE:Synpcc7942_0276
          Length = 490

 Score =  469 bits (1207), Expect = e-136
 Identities = 242/468 (51%), Positives = 315/468 (67%), Gaps = 1/468 (0%)

Query: 19  TSVLMALREHVPGLEILHTDEEIIPYECDGLSAYRTRPLLVVLPKQMEQVTAILAVCHRL 78
           T++  A RE +   +++   EE++ YECDGL+ +R  P LVVLP+  E+V A + +C++ 
Sbjct: 14  TAIAQAFREVLGREQVVERREELLVYECDGLTNHRQIPPLVVLPRSTEEVAAAVRLCNQF 73

Query: 79  RVPVVTRGAGTGLSGGALPLEKGVLLVMARFKEILDINPVGRRARVQPGVRNLAISQAVA 138
            +  V RGAGTGLSGGALP+E  VL+V AR ++IL+I+    R RVQPGV N  ++QA  
Sbjct: 74  DLSFVARGAGTGLSGGALPVEDSVLIVTARMRQILEIDYDNLRVRVQPGVINSWVTQATT 133

Query: 139 PHNLYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLLKIEVQTLDGEALTLGSDA 198
               +YAPDPSSQ  CSIGGNVAEN+GGVHCLK+G+T +++L + +   D   + +G   
Sbjct: 134 GAGFFYAPDPSSQSVCSIGGNVAENSGGVHCLKHGVTNNHVLGLTLVLPDASVIQVGGAI 193

Query: 199 LDSPGFDLLALFTGSEGMLGVTTEVTVKLLPKPPVARVLLASFDSVEKAGLAVGDIIANG 258
            D PG+DL  +F GSEG LG+ TEVT++L P P   +VLLA F S+E AG AV  IIA G
Sbjct: 194 ADLPGYDLCGIFVGSEGTLGIATEVTLRLQPLPQSVQVLLADFSSIEAAGAAVSGIIAAG 253

Query: 259 IIPGGLEMMDNLSIRAAEDFIHAG-YPVDAEAILLCELDGVESDVQEDCERVNDILLKAG 317
           I+P GLE+MDN SI A ED + +  YP DA AILL ELDG  S+V +    V  +  + G
Sbjct: 254 ILPAGLELMDNFSINAVEDVVKSDCYPRDAAAILLAELDGRASEVAQQIRDVEAVCRQHG 313

Query: 318 ATDVRLAQDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPRRALPGVLEGIARLSQQY 377
           A  + +A D  +R+R W GRK AF AVGRISP YY  DG IPR  LP VL  I +L Q++
Sbjct: 314 ARSIAIATDAEDRLRLWKGRKAAFAAVGRISPSYYVQDGVIPRSTLPFVLHEIEQLGQKH 373

Query: 378 DLRVANVFHAGDGNMHPLILFDANEPGEFARAEELGGKILELCVEVGGSISGEHGIGREK 437
             RVANVFHAGDGN+HPLIL+D N+PG   R E LGG+IL+LCV VGGSISGEHGIG +K
Sbjct: 374 GYRVANVFHAGDGNLHPLILYDRNDPGALERVEALGGEILKLCVNVGGSISGEHGIGADK 433

Query: 438 INQMCAQFNSDEITTFHAVKAAFDPDGLLNPGKNIPTLHRCAEFGAMH 485
              M A F+S+++ T   ++ AFDP    NP K  PT   C E G+++
Sbjct: 434 RCYMPAMFSSEDLETMQWLRHAFDPLERANPTKVFPTPRTCGERGSVN 481


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: 728
Number of extensions: 27
Number of successful extensions: 2
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: 490
Length adjustment: 34
Effective length of query: 465
Effective length of database: 456
Effective search space:   212040
Effective search space used:   212040
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.

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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