GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Tatumella morbirosei LMG 23360

Align glucokinase; EC 2.7.1.2 (characterized)
to candidate WP_038019118.1 HA49_RS15320 ROK family protein

Query= CharProtDB::CH_014478
         (324 letters)



>NCBI__GCF_000757425.2:WP_038019118.1
          Length = 406

 Score =  123 bits (309), Expect = 7e-33
 Identities = 87/275 (31%), Positives = 131/275 (47%), Gaps = 9/275 (3%)

Query: 9   VGVDLGGTTIKMAFINHYGEIIHKWEINTDVSEQGRKIPTDIAKAIDKKLNDLGEVKSRL 68
           + V LG     +A  +  G+++ +     D ++Q + +   +  AI+  +     +   L
Sbjct: 89  IAVRLGRQDATLALFDLGGQLLTEQHYPIDQTDQ-QAVEQALFSAIEAFIAQQRPLLDEL 147

Query: 69  VGIGIGAPGPVNFANGSIEVAVNLGWEKFPIKDILEVETSLPVVVDNDANIAAIGEMWKG 128
           + I +  PG V+   G +    ++G   +P+ D L    +    V +D    A+ E + G
Sbjct: 148 IAISVILPGLVDPVQGIVRFMPHIGKTHWPLVDNLTARFNTASFVGHDIRSLALAEHYFG 207

Query: 129 AGDGAKDLLCVTLGTGVGGGVIANGEIVQGVNGAAGEIGHITSIPEGGAPCNCGKTGCLE 188
           A     D L V +  G G G+I NG I  G NG  GEIGHI   P  G  C CG  GCLE
Sbjct: 208 ATRDCADSLLVRIHRGTGAGIIVNGNIFLGTNGNVGEIGHIQVDPL-GERCYCGNFGCLE 266

Query: 189 TIASATGIVRLTMEELTETDKPSELRTVLEQNGQVTSKDVFDAARSKDGLAMHVVDKVAF 248
           TIAS   I++   + L     P +L         +T  D+  AA   D LA  ++ +V  
Sbjct: 267 TIASNNAILQ-KAKTLVAQGYPGKL-----NESTMTISDICQAANQGDPLAQGLIKEVGT 320

Query: 249 HLGLALANSANALNPEKIVLGGGVSRAGEVLLAPV 283
           HLG ALA + N  NP+K+VL G ++ A E +L PV
Sbjct: 321 HLGKALAIAINMFNPQKVVLAGELTEA-EAILFPV 354


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: 271
Number of extensions: 9
Number of successful extensions: 3
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: 406
Length adjustment: 29
Effective length of query: 295
Effective length of database: 377
Effective search space:   111215
Effective search space used:   111215
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