GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaK' in Desulfovibrio vulgaris Hildenborough

Align triokinase (EC 2.7.1.28); glycerone kinase (EC 2.7.1.29); FAD-AMP lyase (cyclizing) (EC 4.6.1.15) (characterized)
to candidate 206411 DVU0979 DAK1 domain protein

Query= BRENDA::Q3LXA3
         (575 letters)



>MicrobesOnline__882:206411
          Length = 354

 Score =  234 bits (596), Expect = 6e-66
 Identities = 140/348 (40%), Positives = 198/348 (56%), Gaps = 25/348 (7%)

Query: 4   KKLVNSVAGCADDALAGLVACNPNLQLLQGHRVALRSDLDSLKGRVALLSGGGSGHEPAH 63
           KKL+N+V     + L G+ A +P L++        R+D+    G+VA++SGGGSGHEP H
Sbjct: 2   KKLINAVENVVREQLQGMAAAHPELRVNIDPHYICRADIPD--GKVAIVSGGGSGHEPMH 59

Query: 64  AGFIGKGMLTGVIAGAVFTSPAVGSILAAIRAVAQAGTVGTLLIVKNYTGDRLNFGLARE 123
            GF+G+GML G   G VFTSP    +    +AV +    G L IVKNYTGD +NF  A E
Sbjct: 60  GGFVGRGMLDGACPGEVFTSPTPDQMYECAKAVDRG--AGVLFIVKNYTGDVMNFETAAE 117

Query: 124 QARAEGIPVEMVVIGDDSAF-TVLKKAGRRGLCGTVLIHKVAGALAEAGVGLEEIAKQVN 182
              A+GI V+ ++I DD A    L  AGRRG+  TVL  K+ GA AEAG  L+  A    
Sbjct: 118 LCHADGIKVQNILIDDDVAVKDSLYTAGRRGVGTTVLAEKIVGAAAEAGYDLDRCADLCR 177

Query: 183 VVAKAMGTLGVSLSSCSVPGS-KPTFELSADEVELGLGIHGEAGVRRIKMATADEIVKLM 241
            V +   ++G++L+SC+VP + KPTFEL+ DE+E+G+GIHGE G +R  M T DE+V++M
Sbjct: 178 KVNRYGRSMGMALTSCTVPAAGKPTFELAEDEIEIGIGIHGEPGTQRAAMMTVDELVEVM 237

Query: 242 ----LDHMTNT---------------TNASHVPVQPGSSVVMMVNNLGGLSFLELGIIAD 282
               +D    T                + +  P   G  V+  VN++GG    EL     
Sbjct: 238 ATAIIDDPAYTRTVREFDRAAGDWVEKSLTDEPFAKGDRVIAFVNSMGGTPVSELYAAYR 297

Query: 283 ATVRSLEGRGVKIARALVGTFMSALEMPGISLTLLLVDEPLLKLIDAE 330
                 + RG+ I R L+G ++++LEM G S+TLL VD+ +L   DA+
Sbjct: 298 KLAEICDRRGIVIVRNLIGPYITSLEMQGFSITLLKVDDEMLAFWDAK 345


Lambda     K      H
   0.315    0.130    0.365 

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: 468
Number of extensions: 24
Number of successful extensions: 6
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: 575
Length of database: 354
Length adjustment: 33
Effective length of query: 542
Effective length of database: 321
Effective search space:   173982
Effective search space used:   173982
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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