GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Caldicellulosiruptor hydrothermalis 108

Align fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_013402581.1 CALHY_RS03245 carbohydrate kinase

Query= BRENDA::O04897
         (347 letters)



>NCBI__GCF_000166355.1:WP_013402581.1
          Length = 312

 Score =  200 bits (509), Expect = 4e-56
 Identities = 123/316 (38%), Positives = 180/316 (56%), Gaps = 16/316 (5%)

Query: 28  VVCFGEMLIDFIPTVAGVSLAEAPAFEKAPGGAPANVAVCISKLGGSSAFIGKVGDDEFG 87
           VVC+GE+LIDF+     +       FE  PGGAPANVA  ++K GG S  I +VG+D FG
Sbjct: 3   VVCYGEVLIDFLNVKENL-------FEANPGGAPANVAAAVAKFGGKSYLISQVGNDMFG 55

Query: 88  RMLADILKQNNVDNSGMRFDHDARTALAFITLTAEGEREFVFFRNPSADMLLRESELDVD 147
           RM+ D L    VD S ++   +  T LAF+ L + GER F F R   AD+ L+  ++D++
Sbjct: 56  RMIIDSLSDCGVDISNVKVTDEYFTTLAFVKLDSRGERSFSFSRKYGADVYLKLEDIDMN 115

Query: 148 LIKKATIFHYGSISLIDEPCRSTHLAAMDIAKRSGSILSYDPNLRLPLWPSEDAARSGIM 207
           ++K A IFH+GS+S+  E  + T L  + IA++SGS +SYDPN R  LW S+  A   ++
Sbjct: 116 IVKSADIFHFGSLSMTYEQNKRTTLELLKIARQSGSTISYDPNYRSSLWESQKKALDTMI 175

Query: 208 S-VWN-LADIIKISEDEISFLTGADDPNDDEVVLKRLFHPNLKLLLVTEGSAGCRYYTKE 265
             V N   DI+K+SE+E+  L    D N+    +K      +K+ LVT G+ G + + KE
Sbjct: 176 EPVENGFVDILKMSEEEV--LLYEKDVNNFYNRIK----DKVKIFLVTFGAKGSKVFFKE 229

Query: 266 FKGRVNSIKVKAVDTTGAGDAFTGGVLKCLASDASLYQ-DEKRLREAIFFANVCAALTVT 324
               V++I+V  VDTTG GD F G VL  ++    +    E  +   +  AN+  AL  T
Sbjct: 230 KSYFVDTIEVNVVDTTGCGDCFVGMVLHEISKSLPIENISENDIINIVKKANIAGALCAT 289

Query: 325 GRGGIPSLPTQDAVRQ 340
            +G IP++P    V +
Sbjct: 290 KKGAIPAIPEYGEVME 305


Lambda     K      H
   0.319    0.135    0.389 

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: 248
Number of extensions: 13
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: 347
Length of database: 312
Length adjustment: 28
Effective length of query: 319
Effective length of database: 284
Effective search space:    90596
Effective search space used:    90596
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 (21.7 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