GapMind for catabolism of small carbon sources

 

Alignments for a candidate for 1pfk in Caldicellulosiruptor kronotskyensis 2002

Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate WP_013431307.1 CALKRO_RS12220 1-phosphofructokinase

Query= reanno::psRCH2:GFF3290
         (312 letters)



>NCBI__GCF_000166775.1:WP_013431307.1
          Length = 315

 Score =  177 bits (450), Expect = 2e-49
 Identities = 103/310 (33%), Positives = 167/310 (53%), Gaps = 1/310 (0%)

Query: 4   VLTVTLNPALDLTVQLPALRLGEVNRSDSLQVHAAGKGLNVAQVLADLGHQLTVTGFLGE 63
           + TVTLNPA+D+TV +  L+ G+VNRS+   + A GKG+NV++V+  LG +    GFLG 
Sbjct: 2   IYTVTLNPAIDMTVYIDELKKGQVNRSNHCLIDAGGKGINVSKVIKSLGGKSIALGFLGN 61

Query: 64  GNPQAFEQLFSARGFTDEFVRVAGETRSNLKLAEADGRV-TDINGPGLAVSEAQRAELLA 122
            N   F +         +F+ V G TR+N+K+ E   +V TD+N  G  V +     L  
Sbjct: 62  DNKDWFLKYLKDLQLDFDFILVDGLTRTNIKIVETAQKVYTDLNQNGFEVKKKDINLLFE 121

Query: 123 RLKRLVPAHELVVVAGSLPRGIDSQWFVQLLNSLKALGVRVALDTSGAALRDGLATRPWL 182
           ++ R+    ++ V++GSLP  +D   +V+L+  LK  G +V  D  G AL  G+  +P +
Sbjct: 122 KIDRIAKTDDIFVLSGSLPPSVDEDVYVELIRMLKRKGAKVIYDADGKALESGVLEKPDV 181

Query: 183 IKPNEEELAEARGIELSGSSALAAEAQRLQEEGIEHVVVSQGADGVSWFSPGAALHASPP 242
           IKPN  E      ++ +  S++ + A+RL E GI+ V++S GA G  + +    L A   
Sbjct: 182 IKPNIHEFKCLFDVDENDLSSIVSSARRLIESGIKKVLISMGAKGAVFVTENMELFAKAA 241

Query: 243 KVRVVSTVGAGDSLLAGMLHGLLEGWPAERTLTHATAIAAQAVGQVGFGITDTAQLAELQ 302
           + +V ST GAGDS++A + +GL +          A A AA  V + G    +  ++    
Sbjct: 242 EAKVKSTTGAGDSMVAAISYGLSQNMDDISIFKLALACAAAKVSKEGVKAPEKNEIEGFL 301

Query: 303 AAVRLQPLSQ 312
             ++L+ L +
Sbjct: 302 EKIKLERLGE 311


Lambda     K      H
   0.316    0.132    0.371 

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: 183
Number of extensions: 7
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate WP_013431307.1 CALKRO_RS12220 (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.2182538.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-105  338.2   0.3   2.2e-105  338.0   0.3    1.0  1  NCBI__GCF_000166775.1:WP_013431307.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_013431307.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  338.0   0.3  2.2e-105  2.2e-105       1     304 [.       2     306 ..       2     307 .. 0.99

  Alignments for each domain:
  == domain 1  score: 338.0 bits;  conditional E-value: 2.2e-105
                             TIGR03828   1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeiealleee 73 
                                           I+TvTlNpaiD+t+ ++el+ g+vnr ++  +dagGKGinV++v+k lg +++algflG+++++ + + l++ 
  NCBI__GCF_000166775.1:WP_013431307.1   2 IYTVTLNPAIDMTVYIDELKKGQVNRSNHCLIDAGGKGINVSKVIKSLGGKSIALGFLGNDNKDWFLKYLKDL 74 
                                           9************************************************************************ PP

                             TIGR03828  74 giktdfvevkgetRinvkikes.sgeetklnepGpeiseeeleallekleeqlkegdvlvlaGSlPrgvpedl 145
                                           +++ df+ v+g tR+n+ki+e+ ++  t+ln++G+e+++++++ l+ek+++ +k++d++vl+GSlP++v+ed+
  NCBI__GCF_000166775.1:WP_013431307.1  75 QLDFDFILVDGLTRTNIKIVETaQKVYTDLNQNGFEVKKKDINLLFEKIDRIAKTDDIFVLSGSLPPSVDEDV 147
                                           **********************9999************************999******************** PP

                             TIGR03828 146 yaelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgvenvli 218
                                           y+eli++l++kgakvi D++g+aL  ++ +kp++iKPN +E++ l++ + ++ +++++ ar+l+e+g+++vli
  NCBI__GCF_000166775.1:WP_013431307.1 148 YVELIRMLKRKGAKVIYDADGKALESGVLEKPDVIKPNIHEFKCLFDVDENDLSSIVSSARRLIESGIKKVLI 220
                                           ************************************************************************* PP

                             TIGR03828 219 slGadGallvtkegalfakapkievkstvGAGDsmvAgfllalekglsleealrlavAvgaaaassegtelpd 291
                                           s+Ga+Ga++vt++ +lfaka++ +vkst+GAGDsmvA++ ++l+++++   +++la+A++aa++s+eg+++p+
  NCBI__GCF_000166775.1:WP_013431307.1 221 SMGAKGAVFVTENMELFAKAAEAKVKSTTGAGDSMVAAISYGLSQNMDDISIFKLALACAAAKVSKEGVKAPE 293
                                           ************************************************************************* PP

                             TIGR03828 292 ledieelleevki 304
                                           +++ie  le++k+
  NCBI__GCF_000166775.1:WP_013431307.1 294 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 19.30
//
[ok]

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