GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Caldicellulosiruptor hydrothermalis 108

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_013403895.1 CALHY_RS10325 ROK family protein

Query= BRENDA::Q8RDE9
         (315 letters)



>NCBI__GCF_000166355.1:WP_013403895.1
          Length = 399

 Score =  170 bits (430), Expect = 6e-47
 Identities = 100/315 (31%), Positives = 168/315 (53%), Gaps = 9/315 (2%)

Query: 5   LCGVDLGGTKISTGIVDENGNII----KSIKIPTMAEKGPDVVIERIEESIYQVLKDTGL 60
           + G+DLG   I   + +  G +I     ++K+    EK  D++ + IE +I +  +    
Sbjct: 80  IIGIDLGVDYIHIILSNFVGEVIFEEYANMKMGEDKEKLLDLLFDLIERAINRAPQTP-- 137

Query: 61  EMSNLKGIGIGSPGPLNAKKGIVISPPNLPHWSNVPIVEILSKRLGIEVRLENDANAAAI 120
               + GIGIG PG +  + GIV+  PNL  W NV +  I+ +R  + V ++N+ANA A+
Sbjct: 138 --KGILGIGIGVPGIVEKESGIVLIAPNLK-WKNVHLKSIVQQRFNLPVYIDNEANAGAL 194

Query: 121 GEHLFGSGRGVDNFVYITVSTGIGGGVIIEGKLYSGENSNAAEIGHHTINFDGPRCNCGN 180
           GE  FG    V + +Y++V  G+G G+II+ KL+ G    A E+GH TINF    C+CGN
Sbjct: 195 GEKWFGEWGKVTDLIYLSVGIGLGAGIIIDNKLFRGAAGFAGEVGHTTINFQDDVCSCGN 254

Query: 181 YGCFEAYASGTAIARFAREGIEKGIKTKIKELAGEGEVKAEHVFEAAKLGDEFAKELVEK 240
            GC E +AS  A+    ++ +++G + +        E+    + +AAK G    +  V +
Sbjct: 255 IGCLENFASERALLSVIKKLVKEGAEDRYISCENVDEITPSQIIQAAKDGSRVCRMAVLE 314

Query: 241 EAFYLGVGIANIMAFYNPRKIAIGGGVSAQWDMLYEKMMETVRKKALKPNAEVCEVVKAQ 300
            A  + +GIAN++  +NP  + IG  VS   D+  EK+ E V +K+        ++  ++
Sbjct: 315 VAEKMAIGIANLVNIFNPEIVIIGNKVSFFGDLFLEKLREVVNQKSFIAQFYDLKIEVSK 374

Query: 301 LGENIGVLGAAALLL 315
           L +   VLG  A+++
Sbjct: 375 LKDRAVVLGCIAMVI 389


Lambda     K      H
   0.316    0.138    0.398 

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: 314
Number of extensions: 15
Number of successful extensions: 2
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: 315
Length of database: 399
Length adjustment: 29
Effective length of query: 286
Effective length of database: 370
Effective search space:   105820
Effective search space used:   105820
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