GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoK in Halococcus hamelinensis 100A6

Align 2-dehydro-3-deoxyglucono/galactono-kinase (EC 2.7.1.178); 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate WP_049904537.1 C447_RS14190 sugar kinase

Query= BRENDA::D4GSE6
         (320 letters)



>NCBI__GCF_000336675.1:WP_049904537.1
          Length = 318

 Score =  166 bits (419), Expect = 9e-46
 Identities = 112/320 (35%), Positives = 161/320 (50%), Gaps = 9/320 (2%)

Query: 4   LVTFGETMLRLSPPRGERLETARELEVQAGGAESNVAVAAARLGRDAAWFSKLPDSPLGR 63
           +VT GETM+ + P     ++ A E E    GAE+NVA+  ARLG D  W+SKL   P G 
Sbjct: 5   VVTLGETMVLVYPSTTGPMKHAHEFEKSLAGAETNVAIGLARLGHDVGWYSKLGTDPHGE 64

Query: 64  RIVSELRSHSVDTDGVVWTDDADARQGVYYLEHGASPRPTNVVYDRADAAVTTLETGEFD 123
            +   +R   VDT  V +TD+A    G+ + E      P  V Y R  +A + +   +  
Sbjct: 65  YLEFFVRGEGVDTTTVEFTDEAPT--GIMFKERREFGEPA-VHYYRHGSAASLMSPDDLP 121

Query: 124 LDAVRDAEVCFTSGITPALSETLSETTADVLDEAQNAGTTTAFDLNYRTKLWSPDE-AAE 182
           +D + +AE    +GITPALSE+  + T    + A  AG T +FD N R KLW  DE   E
Sbjct: 122 VDYLTNAEYLHLTGITPALSESCRDATLLAAERATEAGMTVSFDPNVRRKLWESDERMRE 181

Query: 183 VYRDLLDSVDLLFAAERDAATVLGRDGDAESVARGLADDYDIETVVVTRGEEGSLAVSDG 242
              DL+   D++     + A + G D D E++A     D+   T VV  G  G++ V+DG
Sbjct: 182 TMLDLVSLSDIVLPGIEEGAALFGTD-DPEAIAAACL-DHGAGTAVVKLGAAGAV-VADG 238

Query: 243 AVSEQ-GVYETE-TYDAIGTGDAFVGGFLAKHLDGGSVTESLEWASATASFKRTVEGDIA 300
           + +E+   Y+ E   D +G GD F  GFLA  ++G    E+ E A+A  +F  TV GD  
Sbjct: 239 STTERVSGYDVERVVDPVGAGDGFAAGFLASRIEGQGPVEATETANAVGAFATTVAGDTE 298

Query: 301 VVTPEDVERVVAEEGDGISR 320
            +       V   E D + R
Sbjct: 299 GLPTRKELDVFVGERDAVRR 318


Lambda     K      H
   0.312    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: 277
Number of extensions: 18
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: 320
Length of database: 318
Length adjustment: 28
Effective length of query: 292
Effective length of database: 290
Effective search space:    84680
Effective search space used:    84680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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