GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Echinicola vietnamensis KMM 6221, DSM 17526

Align glucokinase; EC 2.7.1.2 (characterized)
to candidate Echvi_3420 Echvi_3420 Transcriptional regulator/sugar kinase

Query= CharProtDB::CH_014478
         (324 letters)



>FitnessBrowser__Cola:Echvi_3420
          Length = 280

 Score =  100 bits (250), Expect = 3e-26
 Identities = 76/302 (25%), Positives = 132/302 (43%), Gaps = 50/302 (16%)

Query: 9   VGVDLGGTTIKMAFINHYGEIIHKWEINTDVSEQGRKIPTDIAKAIDKKLNDLGE----- 63
           +G+DLGGT +++             E N  +  Q +   T+    ++  L  L E     
Sbjct: 3   IGIDLGGTKVQIGL-----------EKNGTIVRQQKAFLTE-KDNLEASLAQLKEFIRPF 50

Query: 64  VKSRLVGIGIGAPGPVNFANGSIEVAVNL-GWEKFPIKDILEVETSLPVVVDNDANIAAI 122
           +   + GIGIG P  V+ A G +    N+  WEK  +KDILE E ++PV+V+ND N   +
Sbjct: 51  ISEAVSGIGIGVPSVVDTAQGIVYNVTNIPAWEKVHLKDILEEEFNIPVMVNNDVNCFVL 110

Query: 123 GEMWKGAGDGAKDLLCVTLGTGVGGGVIANGEIVQGVNGAAGEIGHITSIPEGGAPCNCG 182
           GE   G G   + ++ + +GTG+G G++ + ++  G N  AGEIG +  + +        
Sbjct: 111 GEHRFGLGKNFQHIVGLCIGTGLGAGLVLDNQLYMGHNCGAGEIGLVPYLDQN------- 163

Query: 183 KTGCLETIASATGIVRLTMEELTETDKPSELRTVLEQNGQVTSKDVFDAARSKDGLAMHV 242
               +E  AS      +                        T+   F AA + D  A+  
Sbjct: 164 ----IEYYASGNFFTAIH---------------------DTTALQAFHAATAGDHDALQQ 198

Query: 243 VDKVAFHLGLALANSANALNPEKIVLGGGVSRAGEVLLAPVRDYFKRFAFPRVAQGAELA 302
            ++   H G A+  +    +PE I++GG +S+A       ++     F +P   +  ++ 
Sbjct: 199 WEEFGLHFGKAMLAAMYTYDPEAIIIGGSISKAYPFFSQALQKTLAEFIYPESFKRLKIL 258

Query: 303 IA 304
           I+
Sbjct: 259 IS 260


Lambda     K      H
   0.316    0.137    0.404 

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: 240
Number of extensions: 17
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 324
Length of database: 280
Length adjustment: 27
Effective length of query: 297
Effective length of database: 253
Effective search space:    75141
Effective search space used:    75141
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 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