GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Novosphingobium barchaimii LL02

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_059152595.1 V474_RS16615 SDR family oxidoreductase

Query= reanno::pseudo1_N1B4:Pf1N1B4_412
         (272 letters)



>NCBI__GCF_001046635.1:WP_059152595.1
          Length = 248

 Score =  141 bits (356), Expect = 1e-38
 Identities = 84/247 (34%), Positives = 132/247 (53%), Gaps = 10/247 (4%)

Query: 20  KNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVV-AIKAD 78
           +++V ++TG A GIGEA+V    ++ A++VI+D   +   ++A  +   GAD   A K D
Sbjct: 5   QDRVAIVTGGASGIGEAVVKDLLAEGAKVVIADFDLDGATRLADTY---GADRARAFKVD 61

Query: 79  VSRQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPL-QMTEEDWHRCFAIDLDGAWYGC 137
           VS  + + A    A+E  G + + VN AG+     PL  +  +DWHR   +DL   +YG 
Sbjct: 62  VSDAEAVEASVAFAVETFGALHLAVNNAGIGAPSTPLADIAIDDWHRVVGVDLHSVFYGM 121

Query: 138 KAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVNA 197
           K  +P M++ G G+I+N+AS        G   Y  +KH ++G+T+   ++YA +GIRVNA
Sbjct: 122 KYQIPAMLKSGGGAIVNMASILGAAGWAGSAAYVTSKHAVVGMTKTAALDYAGQGIRVNA 181

Query: 198 IAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFINA 257
           + P ++ET        G      ER     LH   R+ +P E+A    FL SD A F+  
Sbjct: 182 VGPAFVETPA-----LGKTMTDEERSVLAGLHAFNRLARPEEIAAFTSFLLSDRASFMTG 236

Query: 258 SCITIDG 264
           +   +DG
Sbjct: 237 TYYPVDG 243


Lambda     K      H
   0.321    0.138    0.424 

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: 175
Number of extensions: 14
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: 272
Length of database: 248
Length adjustment: 24
Effective length of query: 248
Effective length of database: 224
Effective search space:    55552
Effective search space used:    55552
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.

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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