GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Halopiger salifodinae KCY07-B2

Align hexokinase (EC 2.7.1.1) (characterized)
to candidate WP_049991158.1 LT39_RS14210 ROK family protein

Query= BRENDA::Q7ZAH1
         (301 letters)



>NCBI__GCF_000784335.1:WP_049991158.1
          Length = 325

 Score =  144 bits (364), Expect = 2e-39
 Identities = 102/309 (33%), Positives = 148/309 (47%), Gaps = 28/309 (9%)

Query: 5   IDVGATWTRVLLVSRDGRVERREKFRTDESP--------VEKAARLVEGW------EFEA 50
           +D+GAT  R ++   DG      +  T   P        V +  R   G          A
Sbjct: 7   VDLGATNVRAVVAEADGTTIGVSRRSTPRGPTGIDVTEGVLRTLRQACGEAGIAPDRIAA 66

Query: 51  IGVGSIGPMDLRRGWVTASPNSPSK--SFPLVEPLLKF--KRPVYVANDCVAAAWGEYVL 106
            G+GSIGP DL  G V    N P+     PL  P+ K      VY+ ND  A   GE   
Sbjct: 67  AGIGSIGPFDLAEGAVIDPANLPNSIDRIPLTGPIGKLIDSDEVYLHNDTTAGVIGERFH 126

Query: 107 GGWGVDNLAYLTLSTGLGVGAVVNGHLILGKEGNAHELGHAVLDVRGDVKCGCGGLGHWE 166
                D++ Y+T+S+G+G G   +G ++ G +GNA E+GH V+D RG + CGCG  GHWE
Sbjct: 127 ADRNPDDMVYITISSGIGAGVCCDGEIMGGWDGNAGEVGHYVVDPRGRLTCGCGREGHWE 186

Query: 167 AMAGGANIPSYFRVFA-------ARLGLRAPEVRTAEDVFKLYREGDRVAQMFVDHWVDV 219
           A   G  IP Y ++ A         L L   +  TA+DVF+L  E D +A   ++     
Sbjct: 187 AYCSGNAIPDYAKLLAEDDPTISTNLPLNGSDF-TAKDVFELAGE-DELADYVIEQLAHW 244

Query: 220 NAAGIATITAAYDPEVLVVGGSIALNHWDLVEAAV-DRLKKYTPLTPPALEKAKFGDDEV 278
           NA G+  +  A+ P V+  GG++AL++ +LV   + +R+ +      P +     GDD V
Sbjct: 245 NAIGVTNVIHAFAPIVVSFGGAVALHNEELVVDPIRERVSEMVMTNVPEIRVTDLGDDVV 304

Query: 279 AMGAAALAI 287
             GA A A+
Sbjct: 305 LEGALASAL 313


Lambda     K      H
   0.320    0.139    0.433 

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: 303
Number of extensions: 24
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: 301
Length of database: 325
Length adjustment: 27
Effective length of query: 274
Effective length of database: 298
Effective search space:    81652
Effective search space used:    81652
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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