GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Mariniradius saccharolyticus AK6

Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate WP_040480287.1 C943_RS09665 ROK family protein

Query= SwissProt::P23917
         (302 letters)



>NCBI__GCF_000330725.2:WP_040480287.1
          Length = 294

 Score = 85.9 bits (211), Expect = 1e-21
 Identities = 77/255 (30%), Positives = 113/255 (44%), Gaps = 32/255 (12%)

Query: 3   IGIDLGGTKTEVIALGDAGEQLYRHRL-PTPRDDYRQTI-ETIATLVDMAEQATGQRGTV 60
           +G+D+GGT  +   L   G +L   R+  TP  + ++ I ETIA L+            +
Sbjct: 9   LGLDIGGTNIKAGVL--VGSELVDIRMIETPSQESQEYILETIADLI--GTYLHHDFFAI 64

Query: 61  GMGIPGSISPYTGVVKNA-NSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAA 119
           G+GIPG I    G+V N  N          + L  R  + V + NDANC A+ E   GAA
Sbjct: 65  GVGIPGLIDTDLGIVLNLENIPSFKRVHLREFLELRFGKPVYINNDANCFALGEYKFGAA 124

Query: 120 AGAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCG 179
              + V  + +GTG GAG+  NG  + G N  AGEW     P++D+D             
Sbjct: 125 KIYKHVVGITLGTGLGAGIIANGHLYCGFNCAAGEW--CSAPYLDQD------------- 169

Query: 180 KQGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSLAHV 239
                E + S   F   Y     HA K   + +  ++ D  A  A   Y   L + + ++
Sbjct: 170 ----FEFYCSSKFFYAKY-----HA-KAKSLSKRAKDGDKEALRAYAEYGHHLGELIKNI 219

Query: 240 VNILDPDVIVLGGGM 254
           +  L P  IVLGG +
Sbjct: 220 LYTLAPQAIVLGGSI 234


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: 250
Number of extensions: 19
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: 302
Length of database: 294
Length adjustment: 26
Effective length of query: 276
Effective length of database: 268
Effective search space:    73968
Effective search space used:    73968
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