Alignments for a candidate for 1pfk in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for 1pfk in Pseudomonas stutzeri RCH2

Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate GFF3290 Psest_3354 1-phosphofructokinase

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



>FitnessBrowser__psRCH2:GFF3290
          Length = 312

 Score =  598 bits (1543), Expect = e-176
 Identities = 312/312 (100%), Positives = 312/312 (100%)

Query: 1   MARVLTVTLNPALDLTVQLPALRLGEVNRSDSLQVHAAGKGLNVAQVLADLGHQLTVTGF 60
           MARVLTVTLNPALDLTVQLPALRLGEVNRSDSLQVHAAGKGLNVAQVLADLGHQLTVTGF
Sbjct: 1   MARVLTVTLNPALDLTVQLPALRLGEVNRSDSLQVHAAGKGLNVAQVLADLGHQLTVTGF 60

Query: 61  LGEGNPQAFEQLFSARGFTDEFVRVAGETRSNLKLAEADGRVTDINGPGLAVSEAQRAEL 120
           LGEGNPQAFEQLFSARGFTDEFVRVAGETRSNLKLAEADGRVTDINGPGLAVSEAQRAEL
Sbjct: 61  LGEGNPQAFEQLFSARGFTDEFVRVAGETRSNLKLAEADGRVTDINGPGLAVSEAQRAEL 120

Query: 121 LARLKRLVPAHELVVVAGSLPRGIDSQWFVQLLNSLKALGVRVALDTSGAALRDGLATRP 180
           LARLKRLVPAHELVVVAGSLPRGIDSQWFVQLLNSLKALGVRVALDTSGAALRDGLATRP
Sbjct: 121 LARLKRLVPAHELVVVAGSLPRGIDSQWFVQLLNSLKALGVRVALDTSGAALRDGLATRP 180

Query: 181 WLIKPNEEELAEARGIELSGSSALAAEAQRLQEEGIEHVVVSQGADGVSWFSPGAALHAS 240
           WLIKPNEEELAEARGIELSGSSALAAEAQRLQEEGIEHVVVSQGADGVSWFSPGAALHAS
Sbjct: 181 WLIKPNEEELAEARGIELSGSSALAAEAQRLQEEGIEHVVVSQGADGVSWFSPGAALHAS 240

Query: 241 PPKVRVVSTVGAGDSLLAGMLHGLLEGWPAERTLTHATAIAAQAVGQVGFGITDTAQLAE 300
           PPKVRVVSTVGAGDSLLAGMLHGLLEGWPAERTLTHATAIAAQAVGQVGFGITDTAQLAE
Sbjct: 241 PPKVRVVSTVGAGDSLLAGMLHGLLEGWPAERTLTHATAIAAQAVGQVGFGITDTAQLAE 300

Query: 301 LQAAVRLQPLSQ 312
           LQAAVRLQPLSQ
Sbjct: 301 LQAAVRLQPLSQ 312


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: 475
Number of extensions: 11
Number of successful extensions: 1
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: 312
Length adjustment: 27
Effective length of query: 285
Effective length of database: 285
Effective search space:    81225
Effective search space used:    81225
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 GFF3290 Psest_3354 (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.9268.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.2e-109  352.0   0.4   1.4e-109  351.8   0.4    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3290  Psest_3354 1-phosphofructokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3290  Psest_3354 1-phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.8   0.4  1.4e-109  1.4e-109       1     304 [.       4     307 ..       4     308 .. 0.99

  Alignments for each domain:
  == domain 1  score: 351.8 bits;  conditional E-value: 1.4e-109
                           TIGR03828   1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeiealleeegi 75 
                                         +lTvTlNpa+D+t++l  l+lgevnr  s +++a+GKG+nVa+vL++lg++ +++gflG+ + + +e+l++++g+
  lcl|FitnessBrowser__psRCH2:GFF3290   4 VLTVTLNPALDLTVQLPALRLGEVNRSDSLQVHAAGKGLNVAQVLADLGHQLTVTGFLGEGNPQAFEQLFSARGF 78 
                                         79************************************************************************* PP

                           TIGR03828  76 ktdfvevkgetRinvkikessgeetklnepGpeiseeeleallekleeqlkegdvlvlaGSlPrgvpedlyaeli 150
                                         +++fv+v+getR+n+k++e +g++t++n+pG ++se++ ++ll++l++ +++++++v+aGSlPrg++++++++l+
  lcl|FitnessBrowser__psRCH2:GFF3290  79 TDEFVRVAGETRSNLKLAEADGRVTDINGPGLAVSEAQRAELLARLKRLVPAHELVVVAGSLPRGIDSQWFVQLL 153
                                         *************************************************************************** PP

                           TIGR03828 151 kllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgvenvlislGadGa 225
                                         + l++ g++v+lDtsg+aL+++l+++p+liKPN+eEl+e+ g el+  +++   a++l+e+g+e+v++s GadG+
  lcl|FitnessBrowser__psRCH2:GFF3290 154 NSLKALGVRVALDTSGAALRDGLATRPWLIKPNEEELAEARGIELSGSSALAAEAQRLQEEGIEHVVVSQGADGV 228
                                         *************************************************************************** PP

                           TIGR03828 226 llvtkegalfakapkievkstvGAGDsmvAgfllalekglsleealrlavAvgaaaassegtelpdledieelle 300
                                          ++++ +al+a++pk++v+stvGAGDs++Ag+l++l +g+++e++l++a+A++a+a+ + g++++d ++++el++
  lcl|FitnessBrowser__psRCH2:GFF3290 229 SWFSPGAALHASPPKVRVVSTVGAGDSLLAGMLHGLLEGWPAERTLTHATAIAAQAVGQVGFGITDTAQLAELQA 303
                                         *************************************************************************99 PP

                           TIGR03828 301 evki 304
                                          v++
  lcl|FitnessBrowser__psRCH2:GFF3290 304 AVRL 307
                                         9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (305 nodes)
Target sequences:                          1  (312 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: 00:00:00.01
# Mc/sec: 8.67
//
[ok]

This GapMind analysis is from Sep 17 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources