GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Bacteroides clarus YIT 12056

Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_009122055.1 BUB52_RS10260 gluconate 5-dehydrogenase

Query= reanno::acidovorax_3H11:Ac3H11_614
         (280 letters)



>NCBI__GCF_900129655.1:WP_009122055.1
          Length = 267

 Score =  103 bits (256), Expect = 5e-27
 Identities = 76/252 (30%), Positives = 119/252 (47%), Gaps = 8/252 (3%)

Query: 33  SLQGRAVFVTGGGSGIGAAIVAAFAEQGARVAFVDVAREASEALAQHIADAGLPRPWWRV 92
           SL+G+   VTG   GIG AI +AFAEQGA++ F D+ +E  +      A+ G+    + V
Sbjct: 8   SLEGKVALVTGASYGIGFAIASAFAEQGAKICFNDINQELVDKGIAAYAEKGIQAHGY-V 66

Query: 93  CDVRDVQALQACMADAAAELGSDFAVLVNNVASDDRHTLESVTPEYYDERMAINERPAFF 152
           CDV D  A+QA +A    E+GS   +LVNN     R  +  +    + + + I+    F 
Sbjct: 67  CDVTDEPAVQAMVATIEKEVGS-VDILVNNAGIIRRIPMHEMEAADFRKVIDIDLNAPFI 125

Query: 153 AIQAVVPGMRRLGAGSVINLGSTGWQGKGTGYPCYAIAKSSVNGLTRGLAKTLGQDRIRI 212
             +AV+P M + G G +IN+ S   +        YA AK  +  LTR +    G+  I+ 
Sbjct: 126 VSKAVLPAMMKKGHGKIINICSMMSELGRETVSAYAAAKGGLKMLTRNICSEYGEYNIQC 185

Query: 213 NTVSPGWVMTERQIKL-WLDAEGEKE-----LARNQCLPDKLRPHDIARMVLFLASDDAA 266
           N + PG++ T +   L    A+G +      +         L P ++    +FLAS+ + 
Sbjct: 186 NGIGPGYIATPQTAPLREKQADGSRHPFDSFICAKTPAGRWLDPEELTGPAVFLASEASN 245

Query: 267 MCTAQEFKVDAG 278
                   VD G
Sbjct: 246 AVNGHILYVDGG 257


Lambda     K      H
   0.320    0.133    0.405 

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: 150
Number of extensions: 10
Number of successful extensions: 3
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: 280
Length of database: 267
Length adjustment: 25
Effective length of query: 255
Effective length of database: 242
Effective search space:    61710
Effective search space used:    61710
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: 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