GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Halococcus hamelinensis 100A6

Align 6-phosphofructokinase (EC 2.7.1.11); 2-dehydro-3-deoxyglucono/galactono-kinase (EC 2.7.1.178); 2-dehydro-3-deoxygalactonokinase (EC 2.7.1.58) (characterized)
to candidate WP_007691604.1 C447_RS05255 sugar kinase

Query= BRENDA::D4GR05
         (318 letters)



>NCBI__GCF_000336675.1:WP_007691604.1
          Length = 314

 Score =  203 bits (516), Expect = 5e-57
 Identities = 129/306 (42%), Positives = 164/306 (53%), Gaps = 5/306 (1%)

Query: 3   AELVTFGETMIRLSPPEGERIETARSLEFRTAGAESNVAVAASRLGCSAAWLSKLPDSPL 62
           A+L+  G +++ L+PPE  R+ETA       AG ESN  +AASRLG  AAW+SKLP +PL
Sbjct: 2   ADLLALGVSVLELTPPEHRRLETAERFAAGVAGPESNTTIAASRLGADAAWVSKLPGNPL 61

Query: 63  GRRVTTELRTHGVEPYVRWDDDARQGAYYIEQGRAPRPTNVIYDRADAAVTTARPDELAV 122
           GRRV   LR HGVE  V W +  RQG  + E+   PR    ++DR +A V + +P +L  
Sbjct: 62  GRRVAGALRRHGVETAVSWAETGRQGLAFTERAGDPRGGMTLHDR-NAPVASMQPADLPA 120

Query: 123 DIVEDAAAFYTSGITPALSETLRETTGELLQTATEAGTTTAFDLNYRSKLWSPSDARDAC 182
              E A+   TSG T  LSETL ETT  + +      TTT   L+ R ++       +A 
Sbjct: 121 TATERASMVLTSGATATLSETLTETTRTVFEECAAGETTTVCSLS-RPRVVESGSVCEAL 179

Query: 183 ESLFPKVDVLVAAERDIRAVLELDGDAPT-LASELAGDFDFETVVVTRGEDGALARHGGT 241
             L    DVL+  E    A   +D   PT  A  LA    FETVV+ R + GA+  H   
Sbjct: 180 SPLLAATDVLLTTEAGAAAF--VDRATPTETAHALAAGHGFETVVLVRADLGAVVWHDNR 237

Query: 242 VYEQPVFETDTVDAIGTGDAFVGAFLSRLIAGEPVETALAYGAATAALKRTVHGDLAVVT 301
           V +  V  TD VD  G  DA  G FL+R IAGE  + ALA G A  AL RTV G +  V 
Sbjct: 238 VDDHDVPATDAVDDRGAFDALCGGFLARRIAGESPDRALAAGVACGALARTVAGPVPTVD 297

Query: 302 PDEVER 307
           P  VER
Sbjct: 298 PAAVER 303


Lambda     K      H
   0.315    0.132    0.378 

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: 295
Number of extensions: 12
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: 318
Length of database: 314
Length adjustment: 27
Effective length of query: 291
Effective length of database: 287
Effective search space:    83517
Effective search space used:    83517
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: 48 (23.1 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