GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Gallaecimonas xiamenensis 3-C-1

Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_008486155.1 B3C1_RS16220 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD

Query= BRENDA::Q1J2J0
         (255 letters)



>NCBI__GCF_000299915.1:WP_008486155.1
          Length = 249

 Score =  149 bits (377), Expect = 4e-41
 Identities = 94/248 (37%), Positives = 131/248 (52%), Gaps = 10/248 (4%)

Query: 13  LFRLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTFERLNVT 72
           +F L+G+ ALVTG ++G+G  +A GLA+ GA V  A       +    ++     +    
Sbjct: 1   MFALNGKRALVTGASRGLGQAMALGLAENGAEVICASSREGGCDDTVAKILALGGKARAL 60

Query: 73  DAD--------AVADLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWC 124
            AD        A+A+ A     VDVLVNN G +    A D P D + AV+ VNL+  F  
Sbjct: 61  AADLGDSQAVQALAEQALAAGPVDVLVNNGGCIYREAALDFPLDAFDAVIKVNLNAAFQL 120

Query: 125 CREFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVR 184
            +  GR M+ +G G IV+ ASM         P  AY ASK A+  LT++LA EW   G++
Sbjct: 121 SQLLGRAMVTKGSGKIVNIASMLSYSGGIRVP--AYTASKHAIAGLTKALANEWGQHGIQ 178

Query: 185 VNAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGH 244
           VNA+APGY  T  T+   +  E      K  P GR   P ++  AV++LAS A+ +V GH
Sbjct: 179 VNAIAPGYFRTDNTQALQDDAERSSEIEKRIPAGRWGNPDDLKGAVVFLASKASDYVNGH 238

Query: 245 TLVVDGGY 252
            L VDGG+
Sbjct: 239 ILAVDGGW 246


Lambda     K      H
   0.319    0.134    0.408 

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: 161
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: 255
Length of database: 249
Length adjustment: 24
Effective length of query: 231
Effective length of database: 225
Effective search space:    51975
Effective search space used:    51975
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: 46 (22.3 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