Aligments for a candidate for 1pfk in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Aligments for a candidate for 1pfk in Pseudomonas fluorescens FW300-N2E3

Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate AO353_05480 AO353_05480 1-phosphofructokinase

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



>FitnessBrowser__pseudo3_N2E3:AO353_05480
          Length = 313

 Score =  510 bits (1313), Expect = e-149
 Identities = 260/313 (83%), Positives = 279/313 (89%)

Query: 1   MAKILTLTLNPALDLTVELARLEPGQVNRSDAMHAHAAGKGVNVAQVLADLGHTLTVSGF 60
           MAKILTLTLNPALDLTV+L  LEPGQVNRSDAMH HAAGKG+NVAQVLADLGH LTVSGF
Sbjct: 1   MAKILTLTLNPALDLTVQLPHLEPGQVNRSDAMHTHAAGKGINVAQVLADLGHQLTVSGF 60

Query: 61  LGEDNAQVFETLFAQRGFVDAFIRVPGETRSNIKLAEQDGRITDLNGPGPMVDAAAQQAL 120
           LGEDN Q FE LFA+RGFVDAFIRVPGETRSNIKLAE DGRITD+NGPGP+V AAAQQAL
Sbjct: 61  LGEDNLQAFEALFAKRGFVDAFIRVPGETRSNIKLAEADGRITDINGPGPVVSAAAQQAL 120

Query: 121 LARLEQIAPGHDVVVVAGSLPRGVSPQWLQALIARMKALGLNVALDTSGEALRVALAAGP 180
           L RL+QI  GHD VVVAGSLPRGVS QWL  L+ R+K+ GL VALDTSGEALR  L+AGP
Sbjct: 121 LDRLDQITLGHDAVVVAGSLPRGVSAQWLHGLLLRLKSRGLKVALDTSGEALRAGLSAGP 180

Query: 181 WLIKPNTEELADALGCEVVSETAQAQAAQRLHAQGIEHVVISHGADGVNWFSVGAALHAS 240
           WLIKPNTEEL++AL CE +S  AQA+AA RLHA GIEHVVISHGA+GVNWFSVG+A+HA+
Sbjct: 181 WLIKPNTEELSEALDCEAISVAAQAEAASRLHAHGIEHVVISHGAEGVNWFSVGSAMHAT 240

Query: 241 PPKVSVASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIHDTALLAS 300
           PP+VSV STVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGI D A LA 
Sbjct: 241 PPRVSVVSTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIGDAAQLAQ 300

Query: 301 LEQGVRVRPLTEQ 313
           LEQ VRVR LTEQ
Sbjct: 301 LEQEVRVRLLTEQ 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: 422
Number of extensions: 15
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 AO353_05480 AO353_05480 (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.11522.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   2.5e-107  344.4   0.5   2.8e-107  344.2   0.5    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05480  AO353_05480 1-phosphofructokinas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_05480  AO353_05480 1-phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.2   0.5  2.8e-107  2.8e-107       1     305 []       4     308 ..       4     308 .. 0.99

  Alignments for each domain:
  == domain 1  score: 344.2 bits;  conditional E-value: 2.8e-107
                                     TIGR03828   1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgee 65 
                                                   IlT+TlNpa+D+t++l +le+g+vnr  +++++a+GKGinVa+vL++lg++ +++gflG+++ + 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05480   4 ILTLTLNPALDLTVQLPHLEPGQVNRSDAMHTHAAGKGINVAQVLADLGHQLTVSGFLGEDNLQA 68 
                                                   89*************************************************************** PP

                                     TIGR03828  66 iealleeegiktdfvevkgetRinvkikessgeetklnepGpeiseeeleallekleeqlkegdv 130
                                                   +eal++++g+ ++f++v+getR+n+k++e +g+ t++n+pGp +s+++++all++l++ +  +d 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05480  69 FEALFAKRGFVDAFIRVPGETRSNIKLAEADGRITDINGPGPVVSAAAQQALLDRLDQITLGHDA 133
                                                   *********************************************************999***** PP

                                     TIGR03828 131 lvlaGSlPrgvpedlyaelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrel 195
                                                   +v+aGSlPrgv+++++  l+ +l+++g+kv+lDtsgeaL+++l+a p+liKPN+eEl+e+l+ e 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05480 134 VVVAGSLPRGVSAQWLHGLLLRLKSRGLKVALDTSGEALRAGLSAGPWLIKPNTEELSEALDCEA 198
                                                   ***************************************************************** PP

                                     TIGR03828 196 kteeevieaarkllekgvenvlislGadGallvtkegalfakapkievkstvGAGDsmvAgflla 260
                                                    + ++  eaa +l+++g+e+v+is Ga+G+ +++   a++a++p+++v+stvGAGDs++Ag+l++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05480 199 ISVAAQAEAASRLHAHGIEHVVISHGAEGVNWFSVGSAMHATPPRVSVVSTVGAGDSLLAGMLHG 263
                                                   ***************************************************************** PP

                                     TIGR03828 261 lekglsleealrlavAvgaaaassegtelpdledieelleevkie 305
                                                   l +  ++e++lr+a+A++a a+++ g++++d +++++l++ev+++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05480 264 LLSADTPEQTLRTATAIAAMAVTQIGFGIGDAAQLAQLEQEVRVR 308
                                                   ******************************************995 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.71
//
[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, or view the source code.

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