GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Saccharomonospora marina XMU15

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_009153825.1 SACMADRAFT_RS10680 ROK family protein

Query= BRENDA::P0A4E1
         (317 letters)



>NCBI__GCF_000244955.1:WP_009153825.1
          Length = 317

 Score =  281 bits (718), Expect = 2e-80
 Identities = 140/310 (45%), Positives = 195/310 (62%)

Query: 3   LTIGVDIGGTKIAAGVVDEEGNILSTHKVPTPTTPEAIVDAIASAVEGARVGHEIVAVGI 62
           L IGVD+GGT + AGVVDE+G +L T +V TP+   A+ DA+A  ++  R  HE+ AVG+
Sbjct: 2   LAIGVDVGGTSVRAGVVDEQGALLDTARVGTPSDELALEDAVAGVIDELRNRHEVGAVGL 61

Query: 63  GAAGYVNRQRSTVYFAPNIDWRQEPLKEKVEARVGLPVVVENDANAAAWGEYKFGGGKGH 122
             A +V   R +V FAP++ WR  P+ ++V  RVGLPV +E+DANAAA  E++FG  +G 
Sbjct: 62  AVAAFVRSDRRSVMFAPHLPWRGAPVADRVSKRVGLPVTLEHDANAAAVAEHRFGAARGA 121

Query: 123 RNVICITLGTGLGGGIIIGNKLRRGHFGVAAEFGHIRMVPDGLLCGCGSQGCWEQYASGR 182
           R    + +GTG+G G+++  +L RG  GVA E GH+ +VP G  C CG  GCWE+Y SG 
Sbjct: 122 RVAALVAIGTGIGAGLLLDGRLFRGAHGVAPELGHLCVVPGGRACPCGKHGCWERYCSGT 181

Query: 183 ALVRYAKQRANATPERAEVLLALGDGTPDGIEGKHISVAARQGCPVAVDSYRELARWAGA 242
           AL   A +     P R+ VL     G P  I G+ ++ AAR G P+A  +  ELARW G 
Sbjct: 182 ALAATAVELLARHPGRSTVLAWETAGDPGSITGRRVAGAARDGDPIAQRAMAELARWLGE 241

Query: 243 GLADLASLFDPSAFIVGGGLSDEGDLVLDPIRKSYKRWLVGGNWRPVADVIAAQLGNKAG 302
           GLA +A ++DP   ++ GG+S+   L LD  R+ Y R + G   RP+A +  +QLG++  
Sbjct: 242 GLALVADVYDPEVVVIAGGVSESAPLFLDEAREHYARAVTGAGHRPLARIRTSQLGDETA 301

Query: 303 LVGAADLARE 312
           LVGAA LARE
Sbjct: 302 LVGAAALARE 311


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: 364
Number of extensions: 17
Number of successful extensions: 1
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: 317
Length adjustment: 27
Effective length of query: 290
Effective length of database: 290
Effective search space:    84100
Effective search space used:    84100
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