GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Vagococcus penaei CD276

Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate WP_077274914.1 BW732_RS00300 D-threitol dehydrogenase

Query= SwissProt::Q92RN6
         (256 letters)



>NCBI__GCF_001998885.1:WP_077274914.1
          Length = 254

 Score =  127 bits (318), Expect = 3e-34
 Identities = 77/244 (31%), Positives = 132/244 (54%), Gaps = 5/244 (2%)

Query: 11  LRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFIQA 70
           L ++  ++TGG SGIG+A+ E + ++GA++A  DI  ++     E V  Q G        
Sbjct: 12  LENKVAIITGGLSGIGSAIGELYVKKGAKLAIFDINPDTP----ELVEEQFGTKAIGFAV 67

Query: 71  DLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFFMC 130
           D+ + E V  A  E +     + +LVN+A        E ++E  WD + ++N++  F + 
Sbjct: 68  DVTSKEQVMNAVKETMNHFKKIDILVNSAGVCFLDDAENLSETEWDLTFNINVKGSFLVA 127

Query: 131 QAVAPHMQRQGGGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDNIRVNA 190
           QAV   M + GGG I+N +S A L+ +    AY+ +K  I+ +TK LA +    +I VN 
Sbjct: 128 QAVGNEMIQSGGGKIINMASQAALVALDNHVAYAASKGAILSMTKVLAYEWAQYSINVNC 187

Query: 191 ILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMTAQAMI 250
           + P +++TE  ++ W  +     M+++  + R    +++    LFLASD+S  MT + M+
Sbjct: 188 LSPTIVLTELGKKAWAGQVG-EDMKQQIPIGRFGYPEEVAASALFLASDASNLMTGENMV 246

Query: 251 IDGG 254
           IDGG
Sbjct: 247 IDGG 250


Lambda     K      H
   0.321    0.133    0.377 

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: 119
Number of extensions: 7
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: 256
Length of database: 254
Length adjustment: 24
Effective length of query: 232
Effective length of database: 230
Effective search space:    53360
Effective search space used:    53360
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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