GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Granulicella mallensis MP5ACTX8

Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate WP_044176839.1 ACIX8_RS15175 fructokinase

Query= SwissProt::P23917
         (302 letters)



>NCBI__GCF_000178955.2:WP_044176839.1
          Length = 301

 Score =  363 bits (932), Expect = e-105
 Identities = 181/302 (59%), Positives = 220/302 (72%), Gaps = 3/302 (0%)

Query: 1   MRIGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQRGTV 60
           MRIGIDLGGTK E IAL   G++L R R+ TPR DY  T+ TIA LV   EQAT + G+V
Sbjct: 1   MRIGIDLGGTKIEAIALDAKGQELRRIRVATPRGDYDATVSTIAGLVHDMEQATKRVGSV 60

Query: 61  GMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAAA 120
           G+GIPG+I   TG+VKNANSTW+NG+PF  DLS  L+REVR ANDANC AVSEA DGAA 
Sbjct: 61  GVGIPGTIIESTGLVKNANSTWINGRPFQHDLSVALEREVRCANDANCFAVSEATDGAAR 120

Query: 121 GAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCGK 180
           GA+ VF VI+GTGCG GVA +GR H G NG AGEWGH PLPW   DE+   +   CYCG+
Sbjct: 121 GARIVFGVIVGTGCGGGVAIDGRVHAGRNGIAGEWGHIPLPWAQGDEVPGPQ---CYCGR 177

Query: 181 QGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSLAHVV 240
            GC+ET+ISGTGF  D+ R +G  L G EI+   E  D  A  AL R E R+A+ LA ++
Sbjct: 178 TGCLETWISGTGFEQDFARRTGRDLLGKEIVAAAEAGDAEALDALDRLEDRMARGLAIMI 237

Query: 241 NILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGVRGAAWLWP 300
           +ILDPDVIV+GGG+SN++RLY  + + ++ + FGG  +TPV +A HGDSSGVRGAAWLW 
Sbjct: 238 DILDPDVIVMGGGLSNIERLYAGISRRLRDYPFGGGVDTPVVRAVHGDSSGVRGAAWLWQ 297

Query: 301 QE 302
            E
Sbjct: 298 PE 299


Lambda     K      H
   0.318    0.137    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: 361
Number of extensions: 16
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: 302
Length of database: 301
Length adjustment: 27
Effective length of query: 275
Effective length of database: 274
Effective search space:    75350
Effective search space used:    75350
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