Alignments for a candidate for 1pfk in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for 1pfk in Pseudomonas fluorescens GW456-L13

Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate PfGW456L13_5074 1-phosphofructokinase (EC 2.7.1.56)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5074
          Length = 312

 Score =  523 bits (1346), Expect = e-153
 Identities = 271/313 (86%), Positives = 285/313 (91%), Gaps = 1/313 (0%)

Query: 1   MAKILTLTLNPALDLTVELARLEPGQVNRSDAMHAHAAGKGVNVAQVLADLGHTLTVSGF 60
           MA+ILTLTLNPALDLTV+L RL+ GQVNRSD MH HAAGKGVNVAQVLADLGH LTVSGF
Sbjct: 1   MARILTLTLNPALDLTVQLPRLDAGQVNRSDVMHTHAAGKGVNVAQVLADLGHQLTVSGF 60

Query: 61  LGEDNAQVFETLFAQRGFVDAFIRVPGETRSNIKLAEQDGRITDLNGPGPMVDAAAQQAL 120
           LGEDN Q FETLFA+RGFVDAFIRVPGETRSNIKLAE DGRITD+NGPGP V  AAQQAL
Sbjct: 61  LGEDNLQAFETLFAKRGFVDAFIRVPGETRSNIKLAESDGRITDINGPGPQVSEAAQQAL 120

Query: 121 LARLEQIAPGHDVVVVAGSLPRGVSPQWLQALIARMKALGLNVALDTSGEALRVALAAGP 180
           + RLEQIAPGHD VVVAGSLP GVS QWLQALI R+K LGLNVALDTSGEALR AL AGP
Sbjct: 121 MDRLEQIAPGHDAVVVAGSLPLGVSAQWLQALILRLKNLGLNVALDTSGEALRAALKAGP 180

Query: 181 WLIKPNTEELADALGCEVVSETAQAQAAQRLHAQGIEHVVISHGADGVNWFSVGAALHAS 240
           WLIKPNTEELA+ LG EVVS +AQA AA+RLHAQGIEHVVISHG DGVNWFSVG+ALHA+
Sbjct: 181 WLIKPNTEELAEVLG-EVVSVSAQALAAERLHAQGIEHVVISHGVDGVNWFSVGSALHAT 239

Query: 241 PPKVSVASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIHDTALLAS 300
           PP+V+VASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGI D A LA 
Sbjct: 240 PPRVNVASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIGDAAQLAQ 299

Query: 301 LEQGVRVRPLTEQ 313
           LEQGVRVRPLTEQ
Sbjct: 300 LEQGVRVRPLTEQ 312


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: 434
Number of extensions: 14
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: 313
Length of database: 312
Length adjustment: 27
Effective length of query: 286
Effective length of database: 285
Effective search space:    81510
Effective search space used:    81510
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 PfGW456L13_5074 (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.15585.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   1.6e-106  341.7   1.7   1.8e-106  341.5   1.7    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5074  1-phosphofructokinase (EC 2.7.1.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5074  1-phosphofructokinase (EC 2.7.1.56)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.5   1.7  1.8e-106  1.8e-106       1     304 [.       4     306 ..       4     307 .. 0.98

  Alignments for each domain:
  == domain 1  score: 341.5 bits;  conditional E-value: 1.8e-106
                                               TIGR03828   1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevval 55 
                                                             IlT+TlNpa+D+t++l +l++g+vnr   ++++a+GKG+nVa+vL++lg++ +++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5074   4 ILTLTLNPALDLTVQLPRLDAGQVNRSDVMHTHAAGKGVNVAQVLADLGHQLTVS 58 
                                                             89***************************************************** PP

                                               TIGR03828  56 gflGgftgeeiealleeegiktdfvevkgetRinvkikessgeetklnepGpeis 110
                                                             gflG+++ + +e+l++++g+ ++f++v+getR+n+k++es+g+ t++n+pGp++s
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5074  59 GFLGEDNLQAFETLFAKRGFVDAFIRVPGETRSNIKLAESDGRITDINGPGPQVS 113
                                                             ******************************************************* PP

                                               TIGR03828 111 eeeleallekleeqlkegdvlvlaGSlPrgvpedlyaelikllrekgakvilDts 165
                                                             e++++al+++le+ ++ +d +v+aGSlP gv++++++ li +l++ g++v+lDts
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5074 114 EAAQQALMDRLEQIAPGHDAVVVAGSLPLGVSAQWLQALILRLKNLGLNVALDTS 168
                                                             ************999**************************************** PP

                                               TIGR03828 166 geaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgvenvlisl 220
                                                             geaL+++lka p+liKPN+eEl+e+lg+ ++  ++   aa++l+++g+e+v+is 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5074 169 GEALRAALKAGPWLIKPNTEELAEVLGEVVSV-SAQALAAERLHAQGIEHVVISH 222
                                                             ***************************99965.66777999************** PP

                                               TIGR03828 221 GadGallvtkegalfakapkievkstvGAGDsmvAgfllalekglsleealrlav 275
                                                             G dG+ +++   al+a++p+++v+stvGAGDs++Ag+l++l +  ++e++lr+a+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5074 223 GVDGVNWFSVGSALHATPPRVNVASTVGAGDSLLAGMLHGLLSADTPEQTLRTAT 277
                                                             ******************************************************* PP

                                               TIGR03828 276 Avgaaaassegtelpdledieelleevki 304
                                                             A++a a+++ g++++d +++++l++ v++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5074 278 AIAAMAVTQIGFGIGDAAQLAQLEQGVRV 306
                                                             ***************************98 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.06
//
[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