GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Weissella oryzae SG25

Align Fructokinase-1; ZmFRK1; EC 2.7.1.4 (characterized)
to candidate WP_027699314.1 TT13_RS06945 ribokinase

Query= SwissProt::Q6XZ79
         (323 letters)



>NCBI__GCF_000691805.2:WP_027699314.1
          Length = 306

 Score =  120 bits (302), Expect = 3e-32
 Identities = 92/287 (32%), Positives = 139/287 (48%), Gaps = 26/287 (9%)

Query: 38  GGAPANVAIAVSRLGGGAAFVGKLGDDEFGRMLAAILRDNGVDDGGVVFDSGARTALAFV 97
           GG  AN A+A +R GG  +FVG +G DE G     +LR+ G+D  G+V      T  A +
Sbjct: 38  GGKGANQAVAAARQGGQVSFVGAVGADEAGERFKKVLREEGIDVSGIVTKK-VPTGSASI 96

Query: 98  TLRADGEREFMFYRNPSADMLLTADELNVELIKRAAVFHYGSISLIA-EPCRTAHLRAME 156
            L  DG    M Y   +A+  LTAD++    +K   +     + +   E  + A  +A  
Sbjct: 97  LLEDDGHNTIMVYGGANAE--LTADDI----VKSENIIANADVVIAQFEVPQEAVAKAFY 150

Query: 157 IAKEAGALLSYDPNLREALWPSREEARTQILSIWDQADIVKVSEVELEFLTGIDSVEDDV 216
            AK+ GAL   +P    A    +E    ++LS     DI+  +E E   L G++   D  
Sbjct: 151 FAKKYGALTILNP----APIIEQEAILPEVLS---STDIIVPNETEAAALVGMEPSTDKA 203

Query: 217 VMKLWRPTMKLL-----LVTLGDQGCKYYARDFHGAVPSFKVQQVDTTGAGDAFVGALLQ 271
            +   R  M  L     ++TLG+ G  Y+  D     P FKV+ VDTT AGD F+G+L  
Sbjct: 204 KLAAVREAMAQLTIQKTVITLGEDGVFYHLADEDQVAPIFKVKPVDTTAAGDTFIGSLTV 263

Query: 272 RIVKDPSSLQDEKKLVESIKFANACGAITTTKKGAIPSLPTEAEVLQ 318
            + KD ++        E+IK+++   +I     GA+ S+PT  EVL+
Sbjct: 264 ELNKDLTN------AAEAIKYSSKASSIAIQHFGALQSIPTRREVLK 304


Lambda     K      H
   0.319    0.136    0.388 

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: 222
Number of extensions: 11
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: 323
Length of database: 306
Length adjustment: 27
Effective length of query: 296
Effective length of database: 279
Effective search space:    82584
Effective search space used:    82584
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