GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacC in Caldicellulosiruptor hydrothermalis 108

Align Tagatose-6-phosphate kinase; EC 2.7.1.144; Phosphotagatokinase (uncharacterized)
to candidate WP_013404313.1 CALHY_RS12555 1-phosphofructokinase

Query= curated2:Q5HM37
         (310 letters)



>NCBI__GCF_000166355.1:WP_013404313.1
          Length = 315

 Score =  154 bits (390), Expect = 2e-42
 Identities = 94/282 (33%), Positives = 156/282 (55%), Gaps = 7/282 (2%)

Query: 1   MILTLTLNPSVDISYPLDQFNLDTVNRVSQTSKTAGGKGLNVTRVLSEFGEDVIASGFLG 60
           MI T+TLNP++D++  +D+     VNR +     AGGKG+NV++V+   G   IA GFLG
Sbjct: 1   MIYTVTLNPAIDMTVYIDELKKGQVNRSNHCLIDAGGKGINVSKVIKSLGGKSIALGFLG 60

Query: 61  GALGQYIEEQIETTRIKQAFFKIKGETRNCIAILHEGQQ--TEILEKGPTIELKESEEFK 118
                +  + ++  +I   F  + G TR  I I+   Q+  T++ + G  ++ K+     
Sbjct: 61  NDNKDWFLKYLKNMQIDYDFIFVDGLTRTNIKIVETAQKVYTDLNQNGFEVKKKDINLLF 120

Query: 119 SHLLKLFKETDVAVMSGSLPKGLNTDYYADIVRLAKEQGILTILDSSGQSLEEVLISNVK 178
             + ++ K  D+ V+SGSLP G + D Y +++R+ K +G   I D+ G++LE  ++   K
Sbjct: 121 DKIDRIAKTDDIFVLSGSLPPGTDEDVYVELIRMLKRKGAKVIYDADGKALESGVLE--K 178

Query: 179 PTVIKPNIDELSQLLNYKVTNDIKELKAAVSQPIFNDIEWIIVSLGSEGA-FAKHNQKFY 237
           P VIKPNI E   L + +  ND+  + ++  + I N I+ +++S+GS+GA F   N + +
Sbjct: 179 PDVIKPNIHEFKCLFDVE-ENDLNSIVSSAKKLIENGIKKVLISMGSKGAVFVTENMELF 237

Query: 238 KVNIPNIKVVNPVGSGDSTVAGIASGLIHQQTDEELLKKANA 279
                 +KV +  G+GDS VA I+ GL     D  + K A A
Sbjct: 238 -AKAAEVKVKSTTGAGDSMVAAISYGLSQNMDDVSIFKLALA 278


Lambda     K      H
   0.314    0.134    0.363 

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: 234
Number of extensions: 10
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: 310
Length of database: 315
Length adjustment: 27
Effective length of query: 283
Effective length of database: 288
Effective search space:    81504
Effective search space used:    81504
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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