Alignments for a candidate for 1pfk in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for 1pfk in Pseudomonas putida KT2440

Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate PP_0794 PP_0794 1-phosphofructokinase monomer

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



>FitnessBrowser__Putida:PP_0794
          Length = 315

 Score =  412 bits (1059), Expect = e-120
 Identities = 214/313 (68%), Positives = 242/313 (77%), Gaps = 3/313 (0%)

Query: 1   MAKILTLTLNPALDLTVELARLEPGQVNRSDAMHAHAAGKGVNVAQVLADLGHTLTVSGF 60
           MAKILTLTLNPALD+T+ L  L PGQVNRS A H+HAAGKG+NVAQVLADLGH++TV GF
Sbjct: 1   MAKILTLTLNPALDITIGLDTLRPGQVNRSQAQHSHAAGKGLNVAQVLADLGHSVTVGGF 60

Query: 61  LGEDNAQVFETLFAQRGFVDAFIRVPGETRSNIKLAEQDGRITDLNGPGPMVDAAAQQAL 120
           LG DN Q FE L   RGF D F+RVPGETRSNIKL E DGR+TD+NG GP VD AA+ AL
Sbjct: 61  LGGDNLQPFEALIDGRGFTDCFVRVPGETRSNIKLVEADGRVTDINGQGPEVDEAARSAL 120

Query: 121 LARLEQIAPGHDVVVVAGSLPRGVSPQWLQALIARMKALGLNVALDTSGEALRVALAAGP 180
           L RLEQIAPGHD VVVAGSLPRG+S  W + L+ R+KA GL V LD+SGEALRV L + P
Sbjct: 121 LHRLEQIAPGHDAVVVAGSLPRGISADWFRQLLERLKAQGLKVVLDSSGEALRVGLQSAP 180

Query: 181 WLIKPNTEELADALGCEVVSETAQAQAAQRLHAQGIEHVVISHGADGVNWFSVGAALHAS 240
           WL+KPNTEEL + LG  V + T Q  AA+RL   G+EHVV+S G  GV+WFS   AL A 
Sbjct: 181 WLVKPNTEELGEVLGLAVDNLTQQRAAAKRLLDSGVEHVVVSAGEQGVSWFSRDLALQAR 240

Query: 241 PPKVSVASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIHDTALLAS 300
           PPKV VASTVGAGDSL+AGM+HGLL A+ P QTL  ATAIAA AVTQ+GFGIHD   LA 
Sbjct: 241 PPKVRVASTVGAGDSLVAGMVHGLLLAEAPAQTLTRATAIAAQAVTQVGFGIHDREHLAQ 300

Query: 301 LEQGVRVRPLTEQ 313
           LE  V+   LTEQ
Sbjct: 301 LEAAVQ---LTEQ 310


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: 340
Number of extensions: 12
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: 315
Length adjustment: 27
Effective length of query: 286
Effective length of database: 288
Effective search space:    82368
Effective search space used:    82368
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 PP_0794 PP_0794 (1-phosphofructokinase monomer)
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.32450.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.5e-108  346.1   0.3   8.4e-108  345.9   0.3    1.0  1  lcl|FitnessBrowser__Putida:PP_0794  PP_0794 1-phosphofructokinase mo


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0794  PP_0794 1-phosphofructokinase monomer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.9   0.3  8.4e-108  8.4e-108       1     304 [.       4     307 ..       4     308 .. 0.99

  Alignments for each domain:
  == domain 1  score: 345.9 bits;  conditional E-value: 8.4e-108
                           TIGR03828   1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeiealleeegi 75 
                                         IlT+TlNpa+D ti l++l++g+vnr ++++ +a+GKG+nVa+vL++lg++v++ gflGg++ +++eal++ +g+
  lcl|FitnessBrowser__Putida:PP_0794   4 ILTLTLNPALDITIGLDTLRPGQVNRSQAQHSHAAGKGLNVAQVLADLGHSVTVGGFLGGDNLQPFEALIDGRGF 78 
                                         89************************************************************************* PP

                           TIGR03828  76 ktdfvevkgetRinvkikessgeetklnepGpeiseeeleallekleeqlkegdvlvlaGSlPrgvpedlyaeli 150
                                         ++ fv+v+getR+n+k++e +g++t++n++Gpe++e++  all++le+ ++ +d +v+aGSlPrg+++d++ +l+
  lcl|FitnessBrowser__Putida:PP_0794  79 TDCFVRVPGETRSNIKLVEADGRVTDINGQGPEVDEAARSALLHRLEQIAPGHDAVVVAGSLPRGISADWFRQLL 153
                                         ***********************************************999************************* PP

                           TIGR03828 151 kllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgvenvlislGadGa 225
                                         ++l+++g+kv+lD+sgeaL+ +l++ p+l+KPN+eEl e+lg ++++ ++   aa++ll++gve+v++s G++G+
  lcl|FitnessBrowser__Putida:PP_0794 154 ERLKAQGLKVVLDSSGEALRVGLQSAPWLVKPNTEELGEVLGLAVDNLTQQRAAAKRLLDSGVEHVVVSAGEQGV 228
                                         *************************************************************************** PP

                           TIGR03828 226 llvtkegalfakapkievkstvGAGDsmvAgfllalekglsleealrlavAvgaaaassegtelpdledieelle 300
                                          +++++ al+a++pk++v+stvGAGDs+vAg++++l   + ++++l+ a+A++a+a+++ g+++ d+e++++l++
  lcl|FitnessBrowser__Putida:PP_0794 229 SWFSRDLALQARPPKVRVASTVGAGDSLVAGMVHGLLLAEAPAQTLTRATAIAAQAVTQVGFGIHDREHLAQLEA 303
                                         *************************************************************************99 PP

                           TIGR03828 301 evki 304
                                          v++
  lcl|FitnessBrowser__Putida:PP_0794 304 AVQL 307
                                         9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (305 nodes)
Target sequences:                          1  (315 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: 7.54
//
[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