GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Neiella marina J221

Align glucokinase; EC 2.7.1.2 (characterized)
to candidate WP_087505883.1 CBE68_RS09735 ROK family transcriptional regulator

Query= CharProtDB::CH_014478
         (324 letters)



>NCBI__GCF_002165625.1:WP_087505883.1
          Length = 407

 Score =  112 bits (281), Expect = 1e-29
 Identities = 71/247 (28%), Positives = 126/247 (51%), Gaps = 8/247 (3%)

Query: 65  KSRLVGIGIGAPGPVNFANGSIEVAVNLGWEK-FPIKDILEVETSLPVVVDNDANIAAIG 123
           K +L+ I I  PG +N   G I  + ++  E+ F I D +    ++P  + N     A+ 
Sbjct: 144 KHQLIAIAITCPGLLNTETGVISYSPHIPLEQPFAIADEISAVFNVPCYLGNSTRSLALA 203

Query: 124 EMWKGAGDGAKDLLCVTLGTGVGGGVIANGEIVQGVNGAAGEIGHITSIPEGGAPCNCGK 183
           E + G     +D++ V +  G+G G+I +GE++ G     GEIGHI   P  G  C+CG 
Sbjct: 204 EHYFGNAKDCRDVVVVRIDHGIGAGIIMDGEVLMGQGLNRGEIGHIQVNPL-GERCHCGN 262

Query: 184 TGCLETIASATGIVRLTMEELTETDKPSELRTVLEQNGQVTSKDVFDAARSKDGLAMHVV 243
            GCLET+A+   +V+  +++L ++   + L         +T   +  AA + D LA  V+
Sbjct: 263 FGCLETVAADDAVVK-RVKQLKDSGYATGLSMT-----NLTMSAICQAALAGDQLAQQVL 316

Query: 244 DKVAFHLGLALANSANALNPEKIVLGGGVSRAGEVLLAPVRDYFKRFAFPRVAQGAELAI 303
            + A  +G ALA + N LNP+KI++GG + +  +V+   +    ++       Q  ++  
Sbjct: 317 KETAEAIGKALATTVNLLNPQKIIIGGDIVQGWDVVAPVLNASLQQQTLELFYQRLQVKA 376

Query: 304 ATLGNDA 310
           +T+  D+
Sbjct: 377 STISQDS 383


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: 251
Number of extensions: 11
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: 324
Length of database: 407
Length adjustment: 29
Effective length of query: 295
Effective length of database: 378
Effective search space:   111510
Effective search space used:   111510
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: 49 (23.5 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