GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Paucidesulfovibrio gracilis DSM 16080

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_078715956.1 B5D49_RS01965 3-oxoacyl-[acyl-carrier-protein] reductase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5967
         (272 letters)



>NCBI__GCF_900167125.1:WP_078715956.1
          Length = 247

 Score =  112 bits (281), Expect = 6e-30
 Identities = 77/244 (31%), Positives = 120/244 (49%), Gaps = 7/244 (2%)

Query: 23  VVLLTGAAQGIGEAIVAAFASQQARLVISDI-QAEKVETVAAHWRERGADVHALKADVSN 81
           V L+TG ++GIG A     A+    + ++ + + E  ETV     + G    A++ D S+
Sbjct: 7   VALVTGGSRGIGRACAERLAADGFEVWLTYVSKPEAAETVVQTIADAGGTARAVQLDSSD 66

Query: 82  QQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGCKAVL 141
           ++ + +  +  ++    +  LVN AG+      + M  EDW     I+L GA+   +   
Sbjct: 67  REAVASFFKDEIKGKVHLAALVNNAGITRDGLLIRMKPEDWDSVLDINLTGAFSCLQEAA 126

Query: 142 PQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAIAPG 201
             M  Q  GSIINI+S        G   Y  AK GL+GLT+A   E A +GVRVNA+APG
Sbjct: 127 KIMARQRGGSIINISSVVGQMGNAGQANYVAAKAGLIGLTKAAARELAGRGVRVNAVAPG 186

Query: 202 YIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFINASCIT 261
           +IET +  D       P    +    + P  R+G P ++A    FLA + A +I    + 
Sbjct: 187 FIETDMTKDL------PEKTVESMKTMIPLSRLGSPGDIAAAVSFLAGNGAGYITGQVLA 240

Query: 262 IDGG 265
           ++GG
Sbjct: 241 VNGG 244


Lambda     K      H
   0.321    0.137    0.419 

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: 143
Number of extensions: 4
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: 272
Length of database: 247
Length adjustment: 24
Effective length of query: 248
Effective length of database: 223
Effective search space:    55304
Effective search space used:    55304
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 Apr 09 2024. 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