Alignments for a candidate for 1pfk in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for 1pfk in Pseudomonas fluorescens FW300-N2E2

Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate Pf6N2E2_3338 1-phosphofructokinase (EC 2.7.1.56)

Query= reanno::pseudo5_N2C3_1:AO356_07330
         (313 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3338
          Length = 313

 Score =  590 bits (1520), Expect = e-173
 Identities = 303/313 (96%), Positives = 306/313 (97%)

Query: 1   MAKILTLTLNPALDLTVELARLEPGQVNRSDAMHAHAAGKGVNVAQVLADLGHTLTVSGF 60
           MAKILTLTLNPALDLTVEL RLEPGQVNRSD MHAHAAGKGVNVAQVLADLGHTLTVSGF
Sbjct: 1   MAKILTLTLNPALDLTVELTRLEPGQVNRSDGMHAHAAGKGVNVAQVLADLGHTLTVSGF 60

Query: 61  LGEDNAQVFETLFAQRGFVDAFIRVPGETRSNIKLAEQDGRITDLNGPGPMVDAAAQQAL 120
           LGEDNAQVFETLFAQRGFVDAFIRVPGETRSNIKLAEQDGRITDLNGPGP+VD AAQQAL
Sbjct: 61  LGEDNAQVFETLFAQRGFVDAFIRVPGETRSNIKLAEQDGRITDLNGPGPVVDEAAQQAL 120

Query: 121 LARLEQIAPGHDVVVVAGSLPRGVSPQWLQALIARMKALGLNVALDTSGEALRVALAAGP 180
           LARLEQIAPGHDVVVVAGSLPRGVSPQWLQALI R+K LGLNVALDTSGEALRVALAAGP
Sbjct: 121 LARLEQIAPGHDVVVVAGSLPRGVSPQWLQALITRLKTLGLNVALDTSGEALRVALAAGP 180

Query: 181 WLIKPNTEELADALGCEVVSETAQAQAAQRLHAQGIEHVVISHGADGVNWFSVGAALHAS 240
           WLIKPNTEELADALGCEVVSE AQAQAAQ LHAQG+EHVVISHGADGVNWFSVGAALHAS
Sbjct: 181 WLIKPNTEELADALGCEVVSEAAQAQAAQHLHAQGVEHVVISHGADGVNWFSVGAALHAS 240

Query: 241 PPKVSVASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIHDTALLAS 300
           PPKVSVASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIHDTALLAS
Sbjct: 241 PPKVSVASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIHDTALLAS 300

Query: 301 LEQGVRVRPLTEQ 313
           LEQGVRVRPLTEQ
Sbjct: 301 LEQGVRVRPLTEQ 313


Lambda     K      H
   0.317    0.132    0.373 

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: 486
Number of extensions: 14
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: 313
Length of database: 313
Length adjustment: 27
Effective length of query: 286
Effective length of database: 286
Effective search space:    81796
Effective search space used:    81796
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)

Align candidate Pf6N2E2_3338 (1-phosphofructokinase (EC 2.7.1.56))
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.14355.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.3e-108  348.6   1.5   1.5e-108  348.4   1.5    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3338  1-phosphofructokinase (EC 2.7.1.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3338  1-phosphofructokinase (EC 2.7.1.56)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.4   1.5  1.5e-108  1.5e-108       1     304 [.       4     307 ..       4     308 .. 0.99

  Alignments for each domain:
  == domain 1  score: 348.4 bits;  conditional E-value: 1.5e-108
                                      TIGR03828   1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftge 64 
                                                    IlT+TlNpa+D+t+el +le+g+vnr   ++ +a+GKG+nVa+vL++lg++ +++gflG+++++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3338   4 ILTLTLNPALDLTVELTRLEPGQVNRSDGMHAHAAGKGVNVAQVLADLGHTLTVSGFLGEDNAQ 67 
                                                    89************************************************************** PP

                                      TIGR03828  65 eiealleeegiktdfvevkgetRinvkikessgeetklnepGpeiseeeleallekleeqlkeg 128
                                                     +e+l++++g+ ++f++v+getR+n+k++e++g+ t+ln+pGp ++e++++all++le+ ++ +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3338  68 VFETLFAQRGFVDAFIRVPGETRSNIKLAEQDGRITDLNGPGPVVDEAAQQALLARLEQIAPGH 131
                                                    **********************************************************999*** PP

                                      TIGR03828 129 dvlvlaGSlPrgvpedlyaelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellg 192
                                                    dv+v+aGSlPrgv++++++ li +l+  g++v+lDtsgeaL+ +l+a p+liKPN+eEl+++lg
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3338 132 DVVVVAGSLPRGVSPQWLQALITRLKTLGLNVALDTSGEALRVALAAGPWLIKPNTEELADALG 195
                                                    **************************************************************** PP

                                      TIGR03828 193 relkteeevieaarkllekgvenvlislGadGallvtkegalfakapkievkstvGAGDsmvAg 256
                                                     e+ +e++  +aa++l+++gve+v+is GadG+ +++  +al+a++pk++v+stvGAGDs++Ag
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3338 196 CEVVSEAAQAQAAQHLHAQGVEHVVISHGADGVNWFSVGAALHASPPKVSVASTVGAGDSLLAG 259
                                                    **************************************************************** PP

                                      TIGR03828 257 fllalekglsleealrlavAvgaaaassegtelpdledieelleevki 304
                                                    +l++l +  ++e++lr+a+A++a a+++ g+++ d + +++l++ v++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3338 260 MLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIHDTALLASLEQGVRV 307
                                                    *********************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (305 nodes)
Target sequences:                          1  (313 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: 9.90
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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