GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Paenisporosarcina indica PN2

Align Fructokinase; EC 2.7.1.4 (characterized)
to candidate WP_075620294.1 GY23_RS16555 fructokinase

Query= SwissProt::P26420
         (307 letters)



>NCBI__GCF_001939075.1:WP_075620294.1
          Length = 312

 Score =  192 bits (487), Expect = 1e-53
 Identities = 118/299 (39%), Positives = 163/299 (54%), Gaps = 5/299 (1%)

Query: 9   GDAVVDLLPDGEGR--LLQCPGGAPANVAVGVARLGGDSGFIGRVGDDPFGRFMRHTLAQ 66
           GDA VD + +           GGA  NVAVGVARLG  S FI   GDDP   F+R  L  
Sbjct: 13  GDAFVDYIAEDRTNTSFSMFLGGATVNVAVGVARLGVPSAFITITGDDPTSEFVRGELKF 72

Query: 67  EQVDVNYMRLDAAQRTSTVVVDLDSHGERTFTFMVRPSADLFLQPEDL--PPFAAGQWLH 124
           E+V + Y +L+  +R S V V L    +R F   +  + D+ ++ +DL    F     L+
Sbjct: 73  EEVIMEYAKLEPEKRVSGVYVHLTEDNDRVFHKYIDDAPDIQVEADDLIEEAFEKASILN 132

Query: 125 VCSIALSAEPSRSTTFAALEAIKRAGGYVSFDPNIRSDLWQDPQDLRDCLDRALALADAI 184
           +CS  L    +  T+  A+E  K+ G   SFD NIR   W   +  R+ +      AD +
Sbjct: 133 LCSGTLFHPKALETSRIAVEFAKKHGALFSFDANIRPLRWSSEKQCRETISSFFKDADLL 192

Query: 185 KLSEEELAFISGSDDIVSGIARLNARFQPTLLLVTQGKAGVQAALRGQVSHFPARPVVAV 244
           K + EELAF++ +  +  G+A+L A  +  ++LVT G+ G  AAL GQV H P  PVV V
Sbjct: 193 KFTREELAFLTETQTLEDGLAKL-APLEIPIILVTAGEEGTYAALNGQVQHVPVEPVVPV 251

Query: 245 DTTGAGDAFVAGLLAGLAAHGIPDNLAALAPDLALAQTCGALATTAKGAMTALPYKDDL 303
           DTTGAGDAF+AG+L  +  +G+P  + +L      A   GALATT  GA+TA+P   DL
Sbjct: 252 DTTGAGDAFMAGILRYVHLNGLPKTIKSLIECCTFANRLGALATTKAGALTAMPRLSDL 310


Lambda     K      H
   0.321    0.137    0.406 

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: 184
Number of extensions: 8
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: 307
Length of database: 312
Length adjustment: 27
Effective length of query: 280
Effective length of database: 285
Effective search space:    79800
Effective search space used:    79800
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