GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Salinicoccus carnicancri Crm

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_017548855.1 C792_RS0107525 ROK family glucokinase

Query= BRENDA::H6UH58
         (328 letters)



>NCBI__GCF_000330705.1:WP_017548855.1
          Length = 319

 Score =  321 bits (822), Expect = 2e-92
 Identities = 163/319 (51%), Positives = 209/319 (65%), Gaps = 2/319 (0%)

Query: 4   IILAADVGGTTCKLGIFTPELEQLHKWSIHTDTSDSTGYTLLKGIYDSFVEKVNENNYNF 63
           +ILAAD+GGT+CKLG+F  EL  + KW I TD S+  G  +L  + DSF  K     +  
Sbjct: 3   VILAADIGGTSCKLGVFDEELNLIEKWEIPTDISEE-GSHILADVLDSFRSKEEILGFKV 61

Query: 64  SNVLGVGIGVPGPVDFEKGTVNGAVNLYWPEKVNVREIFEQFVDCPVYVDNDANIAALGE 123
              LG G+G+PGPVDFEKG +NG +NL    K ++  IF +       VDNDAN+AALGE
Sbjct: 62  EECLGTGLGMPGPVDFEKGILNGCINLNIKGKRSIATIFSELSGSAAIVDNDANVAALGE 121

Query: 124 KHKGAGEGADDVVAITLGTGLGGGIISNGEIVHGHNGSGAEIGHFRADFDQRFKCNCGRS 183
           + KGAG G  +VV ITLGTG+GGG+IS G ++HG  GSG EIGH   DFD RF+CNCG+ 
Sbjct: 122 QSKGAGHGHSEVVMITLGTGVGGGVISEGRLIHGTGGSGGEIGHITVDFDGRFQCNCGKK 181

Query: 184 GCIETVASATGVVNLVNFYYPKLTFRSSILELIKENKVTAKAVFDAAKAGDQFCIFITEK 243
           GC+ETVASATG+VNL   Y+      S ++  IKE  +T+KA+ DAA  GD    F+ E+
Sbjct: 182 GCLETVASATGMVNLAG-YHSDDHENSVLIAAIKEGTLTSKAIVDAAMTGDPLAEFVVEE 240

Query: 244 VANYIGYLCSIISVTSNPKYIVLGGGMSTAGPILIENIKTEYHNLTFAPAQFETEIVQAK 303
            A Y+    S ISV +NP Y V GGG+S AG  L + IK  Y +L F PA  + EIV A+
Sbjct: 241 AARYLAVAMSSISVITNPGYFVFGGGVSRAGRYLTDKIKKYYDSLIFPPAADDVEIVMAE 300

Query: 304 LGNDAGITGAAGLIKTYVL 322
           LGNDAG+ GAA L+K Y++
Sbjct: 301 LGNDAGMYGAARLVKQYLI 319


Lambda     K      H
   0.318    0.138    0.409 

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: 309
Number of extensions: 10
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: 328
Length of database: 319
Length adjustment: 28
Effective length of query: 300
Effective length of database: 291
Effective search space:    87300
Effective search space used:    87300
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: 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