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_075618829.1 GY23_RS08840 sugar kinase

Query= BRENDA::Q6VWJ5
         (386 letters)



>NCBI__GCF_001939075.1:WP_075618829.1
          Length = 321

 Score =  157 bits (397), Expect = 4e-43
 Identities = 102/322 (31%), Positives = 172/322 (53%), Gaps = 15/322 (4%)

Query: 68  VVCFGEMLIDFVPTTSGLSLAEAPAFKKAPGGAPANVAVGISRLGGSSAFIGKVGEDEFG 127
           ++  GE ++ F     G  L     F K  GGA +NVA+G++RLG S+ FI +VG++EFG
Sbjct: 7   LITIGETMVLFEAAADG-PLQYIHQFNKKCGGAESNVAIGVTRLGHSAGFISQVGDEEFG 65

Query: 128 YMLAEILKENNVNSDGMRFDPGARTALAFVTLRKDGEREFMFYRNPSADMLLQEDELDLE 187
             +   ++   V++  ++ +    T L      ++G  +  +YR  SA   ++++ELD E
Sbjct: 66  KFVISSIRGEGVDTSRVKINEDFSTGLYIKETLREGSNQVYYYRKGSAASQMKKEELDWE 125

Query: 188 LIRKAKVFHYGSIS-LITEPCKSAHIAAAKAAKDAGVILSYDPNLRLPLWPSAESAREGI 246
            +R+AKV H   I+  +++ C+    A A+ AK+  ++LS+DPN+R  L      A++ +
Sbjct: 126 YLRQAKVIHLTGITPFLSDSCEELIYAVAEFAKENNILLSFDPNIRYKLMSDKPDAKDIV 185

Query: 247 LSIWNTADIIKISEEEISFLTQGEDPYDDNVVRKLYHPNLKLLLVTEGPEGCRYYTK-DF 305
           L I   AD++    +E  +L  G   Y++ + +   +  +  + +  G  G  Y +K D 
Sbjct: 186 LKIAKLADLVMPGIDEAEYLL-GTRDYNE-IAQYFLNAGVSKIAIKNGDIGTYYDSKEDE 243

Query: 306 SGRVKGIKVD-AVDTTGAGDAFVAGILSQLASDVSLLQDEGK-LRDALSFANACGALTVM 363
           +G +  IKVD  VD  GAGD F AG+LS L         EGK L++A++  +  GA+ V 
Sbjct: 244 AGFIPSIKVDRVVDPIGAGDGFAAGLLSGLL--------EGKSLKEAVTMGSTIGAMVVT 295

Query: 364 ERGAIPALPTKEVVLNTLLKSV 385
            +G +  LP +E + N   KSV
Sbjct: 296 VKGDVEGLPRREALENFHRKSV 317


Lambda     K      H
   0.317    0.134    0.382 

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: 209
Number of extensions: 8
Number of successful extensions: 4
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: 386
Length of database: 321
Length adjustment: 29
Effective length of query: 357
Effective length of database: 292
Effective search space:   104244
Effective search space used:   104244
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: 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