GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Pontimonas salivibrio CL-TW6

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_158665540.1 C3B54_RS04755 ROK family protein

Query= BRENDA::P0A4E1
         (317 letters)



>NCBI__GCF_002950575.1:WP_158665540.1
          Length = 300

 Score =  180 bits (457), Expect = 3e-50
 Identities = 113/316 (35%), Positives = 169/316 (53%), Gaps = 28/316 (8%)

Query: 4   TIGVDIGGTKIAAGVVDEEGNILSTHKVPTPTTPEAIVDAIASAVEGARVGHEIVAVGIG 63
           ++G+DIGGT I AG+V   G      +VPTP+ P+AI+D   +  +   V      VG+ 
Sbjct: 3   SLGIDIGGTSIKAGIVGPRGLEGEIRQVPTPSHPDAIIDTTLALAKSFPVQP---TVGVA 59

Query: 64  AAGYVNRQRSTVYFAPNIDWRQEPLKEKVEARVGLPVVVENDANAAAWGEYKFGGGKGHR 123
            A +++  R+ V F+PNI W   PL+ ++E  + LPVV+ENDANAA +GEY  G G+   
Sbjct: 60  VAAFLDPARTHVEFSPNIAWDGRPLRHELEEGLQLPVVLENDANAAGYGEYVLGAGQQAS 119

Query: 124 NVICITLGTGLGGGIIIGNKLRRGHFGVAAEFGHIRMVPDGLLCGCGSQGCWEQYASGRA 183
            ++ +TLGTG+GG +I+  KL  G  GVA E GHI + P G +CGCG +GC E  +SG A
Sbjct: 120 PMVMLTLGTGVGGAVILDGKLLAGARGVAGELGHIVVNPGGAVCGCGQRGCVETVSSGTA 179

Query: 184 LVRYAKQRANATPERAEVLLALGDGTPDGIEGKHISVAARQGCPVAVDSYRELARWAGAG 243
           L+  A+Q             ALG      I   H   A +Q    A +  + L      G
Sbjct: 180 LMTMARQ-------------ALG----IEINSTH---ALKQALVDAPELRKTLLNTMAEG 219

Query: 244 ----LADLASLFDPSAFIVGGGLSDE-GDLVLDPIRKSYKRWLVGGNWRPVADVIAAQLG 298
               L  + ++ DP+  ++GGG+++  G  + D + +     L G        ++ A+LG
Sbjct: 220 IIGALLQIQAVVDPALSVIGGGVTERLGAELFDALDRLKDDALDGRRSVAFPPIVPAELG 279

Query: 299 NKAGLVGAADLAREPD 314
           N AG++GA  LA+  D
Sbjct: 280 NSAGIIGAGLLAQRHD 295


Lambda     K      H
   0.318    0.139    0.426 

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: 341
Number of extensions: 19
Number of successful extensions: 4
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: 317
Length of database: 300
Length adjustment: 27
Effective length of query: 290
Effective length of database: 273
Effective search space:    79170
Effective search space used:    79170
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 (21.7 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