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_013402452.1 CALHY_RS02545 sugar kinase

Query= BRENDA::Q42896
         (328 letters)



>NCBI__GCF_000166355.1:WP_013402452.1
          Length = 316

 Score =  184 bits (467), Expect = 2e-51
 Identities = 115/310 (37%), Positives = 165/310 (53%), Gaps = 12/310 (3%)

Query: 12  IVSFGEMLIDFVPTVSGVSLAEAPGFLKAPGGAPANVAIAVTRLGGKSAFVGKLGDDEFG 71
           +V+ GE ++ F PT SG  L     F+K  GGA AN AI + RLG K+ ++ KLG+DEFG
Sbjct: 4   VVTIGEAMVVFNPTASG-PLRYVNNFVKKVGGAEANFAIGIVRLGHKAGWISKLGNDEFG 62

Query: 72  HMLAGILKTNGVQAEGINFDKGARTALAFVTLRADGEREFMFYRNPSADMLLTPAELNLD 131
             +  +++  GV    + FD  A T + F  +R  GE +  +YR  SA   LTP +L+ D
Sbjct: 63  KCILSVIRGEGVDTSQVKFDPEAPTGIYFKEIREYGETKVYYYRRGSAASRLTPEDLDPD 122

Query: 132 LIRSAKVFHYGSIS-LIVEPCRAAHMKAMEVAKEAGALLSYDPNLRLPLWPSAEEAKKQI 190
            I SAK  H   I+  + E C     +A+++AK  G  +S DPN+RL LW S E+A++ I
Sbjct: 123 YIGSAKYLHVTGITPALSESCYLTIKEAIKIAKSRGVKISLDPNIRLKLW-SKEQARRVI 181

Query: 191 KSIWDSADVIKVSDVELEFLTGSNKIDDESAMSLWHPNLKLLLVTLGEKGCNYYTKKFHG 250
             + + AD++     E E L G  K  +  A       + +++V LGEKG  Y TK   G
Sbjct: 182 MELAEQADIVLPGITEGEILVG-EKNPENIAKKFLDLGVSIVVVKLGEKGAYYATKDESG 240

Query: 251 TVGGFHV-KTVDTTGAGDSFVGALLTKIVDDQTILEDEARLKEVLRFSCACGAITTTKKG 309
            V GF + K VD  GAGD F    +  ++ + +       LKE ++ + A GAI TT  G
Sbjct: 241 YVSGFPIEKVVDPIGAGDGFAAGFIAGLLKNYS-------LKEAVKLANAVGAIATTVIG 293

Query: 310 AIPALPTASE 319
               LPT  E
Sbjct: 294 DFEGLPTMEE 303


Lambda     K      H
   0.318    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: 261
Number of extensions: 14
Number of successful extensions: 7
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: 328
Length of database: 316
Length adjustment: 28
Effective length of query: 300
Effective length of database: 288
Effective search space:    86400
Effective search space used:    86400
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