Alignments for a candidate for 1pfk in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for 1pfk in Pseudomonas fluorescens FW300-N1B4

Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate Pf1N1B4_1145 1-phosphofructokinase (EC 2.7.1.56)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1145
          Length = 313

 Score =  516 bits (1329), Expect = e-151
 Identities = 265/313 (84%), Positives = 279/313 (89%)

Query: 1   MAKILTLTLNPALDLTVELARLEPGQVNRSDAMHAHAAGKGVNVAQVLADLGHTLTVSGF 60
           MAKILTLTLNPALDLTV+L  L  GQVNRSD MH HAAGKGVNVAQVLADLGH LTVSGF
Sbjct: 1   MAKILTLTLNPALDLTVQLPLLTAGQVNRSDEMHTHAAGKGVNVAQVLADLGHQLTVSGF 60

Query: 61  LGEDNAQVFETLFAQRGFVDAFIRVPGETRSNIKLAEQDGRITDLNGPGPMVDAAAQQAL 120
           LGEDN Q FETLFA+RGF DAF+RVPGETRSNIKLAE DGRITD+NGPGP V  AAQQAL
Sbjct: 61  LGEDNLQAFETLFAKRGFTDAFVRVPGETRSNIKLAESDGRITDINGPGPRVSEAAQQAL 120

Query: 121 LARLEQIAPGHDVVVVAGSLPRGVSPQWLQALIARMKALGLNVALDTSGEALRVALAAGP 180
           L RL+QIAPGHD VVVAGSLPRGV+PQWL+ LI R+K  GL VALDTSGEALR  L AGP
Sbjct: 121 LDRLDQIAPGHDAVVVAGSLPRGVNPQWLRELIQRLKKRGLKVALDTSGEALRAGLVAGP 180

Query: 181 WLIKPNTEELADALGCEVVSETAQAQAAQRLHAQGIEHVVISHGADGVNWFSVGAALHAS 240
           WLIKPNTEELA+ALGCEVVS  AQA+AA RLHA GIEHVVIS GADGVNWFSVG+A+HA+
Sbjct: 181 WLIKPNTEELAEALGCEVVSVGAQAEAASRLHAHGIEHVVISDGADGVNWFSVGSAMHAT 240

Query: 241 PPKVSVASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIHDTALLAS 300
           PPKVSV STVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGI D A LA 
Sbjct: 241 PPKVSVISTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIGDAAQLAH 300

Query: 301 LEQGVRVRPLTEQ 313
           LEQGVR+RPLTEQ
Sbjct: 301 LEQGVRLRPLTEQ 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: 427
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 Pf1N1B4_1145 (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.27849.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-109  351.9   0.4   1.4e-109  351.8   0.4    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1145  1-phosphofructokinase (EC 2.7.1.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1145  1-phosphofructokinase (EC 2.7.1.56)
   #    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 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftge 64 
                                                    IlT+TlNpa+D+t++l  l++g+vnr  +++++a+GKG+nVa+vL++lg++ +++gflG+++ +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1145   4 ILTLTLNPALDLTVQLPLLTAGQVNRSDEMHTHAAGKGVNVAQVLADLGHQLTVSGFLGEDNLQ 67 
                                                    89************************************************************** PP

                                      TIGR03828  65 eiealleeegiktdfvevkgetRinvkikessgeetklnepGpeiseeeleallekleeqlkeg 128
                                                     +e+l++++g++++fv+v+getR+n+k++es+g+ t++n+pGp++se++++all++l++ ++ +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1145  68 AFETLFAKRGFTDAFVRVPGETRSNIKLAESDGRITDINGPGPRVSEAAQQALLDRLDQIAPGH 131
                                                    **********************************************************999*** PP

                                      TIGR03828 129 dvlvlaGSlPrgvpedlyaelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellg 192
                                                    d +v+aGSlPrgv+++++ eli++l+++g+kv+lDtsgeaL+++l a p+liKPN+eEl+e+lg
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1145 132 DAVVVAGSLPRGVNPQWLRELIQRLKKRGLKVALDTSGEALRAGLVAGPWLIKPNTEELAEALG 195
                                                    **************************************************************** PP

                                      TIGR03828 193 relkteeevieaarkllekgvenvlislGadGallvtkegalfakapkievkstvGAGDsmvAg 256
                                                     e+ + ++  eaa +l+++g+e+v+is GadG+ +++   a++a++pk++v stvGAGDs++Ag
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1145 196 CEVVSVGAQAEAASRLHAHGIEHVVISDGADGVNWFSVGSAMHATPPKVSVISTVGAGDSLLAG 259
                                                    **************************************************************** PP

                                      TIGR03828 257 fllalekglsleealrlavAvgaaaassegtelpdledieelleevki 304
                                                    +l++l +  ++e++lr+a+A++a a+++ g++++d +++++l++ v++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1145 260 MLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIGDAAQLAHLEQGVRL 307
                                                    *******************************************99986 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.96
//
[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