GapMind for catabolism of small carbon sources

 

Alignments for a candidate for 1pfk in Caldicellulosiruptor hydrothermalis 108

Align 1-phosphofructokinase (characterized)
to candidate WP_013404313.1 CALHY_RS12555 1-phosphofructokinase

Query= CharProtDB::CH_024159
         (312 letters)



>NCBI__GCF_000166355.1:WP_013404313.1
          Length = 315

 Score =  176 bits (447), Expect = 5e-49
 Identities = 107/307 (34%), Positives = 169/307 (55%), Gaps = 3/307 (0%)

Query: 5   VATITLNPAYDLVGFCPEIERGEVNLVKTTGLHAAGKGINVAKVLKDLGIDVTVGGFLGK 64
           + T+TLNPA D+  +  E+++G+VN      + A GKGINV+KV+K LG      GFLG 
Sbjct: 2   IYTVTLNPAIDMTVYIDELKKGQVNRSNHCLIDAGGKGINVSKVIKSLGGKSIALGFLGN 61

Query: 65  DNQDGFQQLFSELGIANRFQVVQGRTRINVKLTEKDGEV-TDFNFSGFEVTPADWERFVT 123
           DN+D F +    + I   F  V G TR N+K+ E   +V TD N +GFEV   D    + 
Sbjct: 62  DNKDWFLKYLKNMQIDYDFIFVDGLTRTNIKIVETAQKVYTDLNQNGFEVKKKDIN-LLF 120

Query: 124 DSLSWLGQFDMVCV-SGSLPSGVSPEAFTDWMTRLRSQCPCIIFDSSREALVAGLKAAPW 182
           D +  + + D + V SGSLP G   + + + +  L+ +   +I+D+  +AL +G+   P 
Sbjct: 121 DKIDRIAKTDDIFVLSGSLPPGTDEDVYVELIRMLKRKGAKVIYDADGKALESGVLEKPD 180

Query: 183 LVKPNRRELEIWAGRKLPEMKDVIEAAHALREQGIAHVVISLGAEGALWVNASGEWIAKP 242
           ++KPN  E +     +  ++  ++ +A  L E GI  V+IS+G++GA++V  + E  AK 
Sbjct: 181 VIKPNIHEFKCLFDVEENDLNSIVSSAKKLIENGIKKVLISMGSKGAVFVTENMELFAKA 240

Query: 243 PSVDVVSTVGAGDSMVGGLIYGLLMRESSEHTLRLATAVAALAVSQSNVGITDRPQLAAM 302
             V V ST GAGDSMV  + YGL          +LA A AA  VS+  V   ++ ++   
Sbjct: 241 AEVKVKSTTGAGDSMVAAISYGLSQNMDDVSIFKLALACAAAKVSKEGVKPPEKNEIEGF 300

Query: 303 MARVDLQ 309
           + ++ L+
Sbjct: 301 LEKIKLE 307


Lambda     K      H
   0.319    0.135    0.404 

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: 227
Number of extensions: 13
Number of successful extensions: 2
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: 312
Length of database: 315
Length adjustment: 27
Effective length of query: 285
Effective length of database: 288
Effective search space:    82080
Effective search space used:    82080
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_013404313.1 CALHY_RS12555 (1-phosphofructokinase)
to HMM TIGR03828 (pfkB: 1-phosphofructokinase (EC 2.7.1.56))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR03828.hmm
# target sequence database:        /tmp/gapView.3456715.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03828  [M=305]
Accession:   TIGR03828
Description: pfkB: 1-phosphofructokinase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-106  341.5   0.4   2.2e-106  341.3   0.4    1.0  1  NCBI__GCF_000166355.1:WP_013404313.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166355.1:WP_013404313.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.3   0.4  2.2e-106  2.2e-106       1     304 [.       2     306 ..       2     307 .. 0.99

  Alignments for each domain:
  == domain 1  score: 341.3 bits;  conditional E-value: 2.2e-106
                             TIGR03828   1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeiealleee 73 
                                           I+TvTlNpaiD+t+ ++el+ g+vnr ++  +dagGKGinV++v+k lg +++algflG+++++ + + l++ 
  NCBI__GCF_000166355.1:WP_013404313.1   2 IYTVTLNPAIDMTVYIDELKKGQVNRSNHCLIDAGGKGINVSKVIKSLGGKSIALGFLGNDNKDWFLKYLKNM 74 
                                           9************************************************************************ PP

                             TIGR03828  74 giktdfvevkgetRinvkikes.sgeetklnepGpeiseeeleallekleeqlkegdvlvlaGSlPrgvpedl 145
                                           +i+ df+ v+g tR+n+ki+e+ ++  t+ln++G+e+++++++ l++k+++ +k++d++vl+GSlP+g +ed+
  NCBI__GCF_000166355.1:WP_013404313.1  75 QIDYDFIFVDGLTRTNIKIVETaQKVYTDLNQNGFEVKKKDINLLFDKIDRIAKTDDIFVLSGSLPPGTDEDV 147
                                           **********************9999************************999******************** PP

                             TIGR03828 146 yaelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgvenvli 218
                                           y+eli++l++kgakvi D++g+aL  ++ +kp++iKPN +E++ l++ e ++ +++++ a+kl+e+g+++vli
  NCBI__GCF_000166355.1:WP_013404313.1 148 YVELIRMLKRKGAKVIYDADGKALESGVLEKPDVIKPNIHEFKCLFDVEENDLNSIVSSAKKLIENGIKKVLI 220
                                           ************************************************************************* PP

                             TIGR03828 219 slGadGallvtkegalfakapkievkstvGAGDsmvAgfllalekglsleealrlavAvgaaaassegtelpd 291
                                           s+G++Ga++vt++ +lfaka++++vkst+GAGDsmvA++ ++l+++++   +++la+A++aa++s+eg++ p+
  NCBI__GCF_000166355.1:WP_013404313.1 221 SMGSKGAVFVTENMELFAKAAEVKVKSTTGAGDSMVAAISYGLSQNMDDVSIFKLALACAAAKVSKEGVKPPE 293
                                           ************************************************************************* PP

                             TIGR03828 292 ledieelleevki 304
                                           +++ie  le++k+
  NCBI__GCF_000166355.1:WP_013404313.1 294 KNEIEGFLEKIKL 306
                                           ********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (305 nodes)
Target sequences:                          1  (315 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 17.73
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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