GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glucosaminate-lyase in Desulfovibrio vulgaris Hildenborough

Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate 207304 DVU1838 thioredoxin reductase

Query= curated2:Q93HX6
         (320 letters)



>MicrobesOnline__882:207304
          Length = 307

 Score =  176 bits (445), Expect = 8e-49
 Identities = 110/308 (35%), Positives = 165/308 (53%), Gaps = 11/308 (3%)

Query: 10  IILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGLTGPALMERM 69
           I++G GPAG +AA+Y AR+ +   ++  +  GGQ+  T+E++N+PG   G+ G  L +  
Sbjct: 7   IVIGGGPAGMTAALYLARSGVSVAMVERLSPGGQVLMTSEIENYPGFPKGIQGWELADLF 66

Query: 70  REHAERFETEIVFDHINAVDFAAKPYTLTGDSATYTCDALIIATGASARYLGLPSEEAFM 129
             H E +      D +  +  A     +       +   LI+ +GA  + LGLP EE   
Sbjct: 67  AAHLEGYAITRFNDEVREIVPAPADNRVRVGDDWISGRTLILCSGARYKRLGLPDEERLT 126

Query: 130 GKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETFRAEKILID 189
           GKGVS CA CDG F+R + V VVGGGN+A+EE+LYL+ +   + LIHRR+ FRA K   D
Sbjct: 127 GKGVSYCALCDGNFFRGQVVGVVGGGNSALEESLYLSKLVKKLHLIHRRDDFRAAKCYQD 186

Query: 190 KLNARVAEGKIILKLNANLDEVLGDN--MGVTGARLKNNDGSFDELKVDGVFIAIGHTPN 247
           K+        I +  ++ ++ + GD+   GVT   +K  + SF  L++DG+FI IG  P 
Sbjct: 187 KV---CIMPDIDVVRSSVVEAIHGDDRLTGVTVRNVKTGETSF--LELDGLFIFIGFEPV 241

Query: 248 TSLFEGQLTLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAGAGCMAALD 307
                G +   +   V+  G       T++ GIFAAGD+   + RQ  T+ G G  AA  
Sbjct: 242 GGFLPGGIERDEQGFVITDGE----MRTNLPGIFAAGDIRSKMCRQVTTAVGDGATAANA 297

Query: 308 TERYLDGL 315
              YL+ L
Sbjct: 298 AFVYLEQL 305


Lambda     K      H
   0.318    0.135    0.386 

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: 284
Number of extensions: 17
Number of successful extensions: 5
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: 307
Length adjustment: 27
Effective length of query: 293
Effective length of database: 280
Effective search space:    82040
Effective search space used:    82040
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 (21.7 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