GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Caldicellulosiruptor kronotskyensis 2002

Align Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 (characterized)
to candidate WP_013430927.1 CALKRO_RS10160 ROK family transcriptional regulator

Query= SwissProt::Q9X1I0
         (317 letters)



>NCBI__GCF_000166775.1:WP_013430927.1
          Length = 399

 Score =  144 bits (363), Expect = 4e-39
 Identities = 93/317 (29%), Positives = 158/317 (49%), Gaps = 19/317 (5%)

Query: 6   LIGVDLGGTTFSVGLVSEDGKILKKVTRDTLVENGKEDVIRRIAETILEVSDGEEAPY-- 63
           +IG+DLG     V L +  G+++ +   +  +   K+ +   + + I +  D   AP+  
Sbjct: 80  IIGIDLGVDYIHVILSNFVGEVIFEEYAEMKMGEDKDKLFDLLFDLIEKAID--RAPHTP 137

Query: 64  -----VGIGSPGSIDRENGIVRFSPNFPDWHNVPLTDELAKRTGKKVFLENDANAFVLGE 118
                +GIG PG +++E+GIV  +PN   W NV L   + +R    V+++N+ANA  LGE
Sbjct: 138 KGILGIGIGVPGIVEKESGIVLIAPNLK-WKNVHLKSIVQQRFNLPVYIDNEANAGALGE 196

Query: 119 KWFGAGRGHDHIVALTLGTGIGGGVVTHGYLLTGRDGIGAELGHVVVEPNGPMCNCGTRG 178
           KWFG       ++ L++G G+G G++    L  G  G   E+GH  +     +C+CG  G
Sbjct: 197 KWFGEWGKVSDLIYLSVGIGLGAGIIIDNKLFRGAAGFAGEVGHTTINFQDDVCSCGNIG 256

Query: 179 CLEAVASATA----IRRFLREGYKKYHSSLVYKLAGSPEKADAKHLFDAARQGDRFALMI 234
           CLE  AS  A    I++ +++G +  + S       +  +     +  AA++G R   M 
Sbjct: 257 CLENFASERALLSVIKKLVKQGVEDRYIS-----CENVHEITPSRIIQAAKEGSRVCRMA 311

Query: 235 RDRVVDALARAVAGYIHIFNPEIVIIGGGISRAGEILFGPLREKVVDYIMPSFVGTYEVV 294
              V + +   VA  ++IFNPE+VIIG   S  GE+    LRE +      +     ++ 
Sbjct: 312 ILEVAEKMGIGVANLVNIFNPEMVIIGNKASFFGELFLEKLREVINQRSFIAQFYNLKIE 371

Query: 295 ASPLVEDAGILGAASII 311
            S L + A +LG  +++
Sbjct: 372 VSKLKDRAVVLGCIAMV 388


Lambda     K      H
   0.320    0.142    0.418 

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: 311
Number of extensions: 14
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: 317
Length of database: 399
Length adjustment: 29
Effective length of query: 288
Effective length of database: 370
Effective search space:   106560
Effective search space used:   106560
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 (21.7 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