Alignments for a candidate for 1pfk in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for 1pfk in Pseudomonas simiae WCS417

Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate GFF781 PS417_03970 1-phosphofructokinase

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



>FitnessBrowser__WCS417:GFF781
          Length = 306

 Score =  447 bits (1149), Expect = e-130
 Identities = 232/313 (74%), Positives = 255/313 (81%), Gaps = 7/313 (2%)

Query: 1   MAKILTLTLNPALDLTVELARLEPGQVNRSDAMHAHAAGKGVNVAQVLADLGHTLTVSGF 60
           MA+ILTLTLNPALDLTV LARLEPG+VNRS+ +  HAAGKGVNVAQVLADLGH LTVSGF
Sbjct: 1   MARILTLTLNPALDLTVRLARLEPGEVNRSETLLTHAAGKGVNVAQVLADLGHELTVSGF 60

Query: 61  LGEDNAQVFETLFAQRGFVDAFIRVPGETRSNIKLAEQDGRITDLNGPGPMVDAAAQQAL 120
           LGE N Q FE L AQRGF DAFIRVPGETRSNIK+AEQDGR+TD+N PGP V   AQ AL
Sbjct: 61  LGEGNPQAFEALIAQRGFTDAFIRVPGETRSNIKIAEQDGRVTDINAPGPQVTEQAQNAL 120

Query: 121 LARLEQIAPGHDVVVVAGSLPRGVSPQWLQALIARMKALGLNVALDTSGEALRVALAAGP 180
           L +L QIAPG D VVVAGSLPRGVSPQW + L+ ++K  GL VALDTSGEALR  L AGP
Sbjct: 121 LDKLAQIAPGFDAVVVAGSLPRGVSPQWFKGLLEQLKRYGLKVALDTSGEALRAGLLAGP 180

Query: 181 WLIKPNTEELADALGCEVVSETAQAQAAQRLHAQGIEHVVISHGADGVNWFSVGAALHAS 240
           WL+KPNTEELA+AL            A  +LH QG+EHVV+S GA GV+W+S  AAL A+
Sbjct: 181 WLVKPNTEELAEAL-------DNATDAVSQLHRQGVEHVVVSDGAAGVSWYSPNAALQAT 233

Query: 241 PPKVSVASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIHDTALLAS 300
           PPKV+VASTVGAGDSLLAGMLHGLL+ DTPEQTLR ATAIAAMAVTQIGFGI D A LA 
Sbjct: 234 PPKVTVASTVGAGDSLLAGMLHGLLTGDTPEQTLRRATAIAAMAVTQIGFGISDHAQLAR 293

Query: 301 LEQGVRVRPLTEQ 313
           LE GV+VR LTEQ
Sbjct: 294 LESGVQVRSLTEQ 306


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: 399
Number of extensions: 8
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: 306
Length adjustment: 27
Effective length of query: 286
Effective length of database: 279
Effective search space:    79794
Effective search space used:    79794
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 GFF781 PS417_03970 (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.30404.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-104  335.5   0.4   1.4e-104  335.3   0.4    1.0  1  lcl|FitnessBrowser__WCS417:GFF781  PS417_03970 1-phosphofructokinas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF781  PS417_03970 1-phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.3   0.4  1.4e-104  1.4e-104       1     304 [.       4     300 ..       4     301 .. 0.99

  Alignments for each domain:
  == domain 1  score: 335.3 bits;  conditional E-value: 1.4e-104
                          TIGR03828   1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeiealleeegik 76 
                                        IlT+TlNpa+D+t++l +le+gevnr e+  ++a+GKG+nVa+vL++lg+e +++gflG+ + + +eal++++g++
  lcl|FitnessBrowser__WCS417:GFF781   4 ILTLTLNPALDLTVRLARLEPGEVNRSETLLTHAAGKGVNVAQVLADLGHELTVSGFLGEGNPQAFEALIAQRGFT 79 
                                        89************************************************************************** PP

                          TIGR03828  77 tdfvevkgetRinvkikessgeetklnepGpeiseeeleallekleeqlkegdvlvlaGSlPrgvpedlyaelikl 152
                                        ++f++v+getR+n+ki+e++g++t++n+pGp+++e++++all+kl++ ++  d +v+aGSlPrgv++++++ l+++
  lcl|FitnessBrowser__WCS417:GFF781  80 DAFIRVPGETRSNIKIAEQDGRVTDINAPGPQVTEQAQNALLDKLAQIAPGFDAVVVAGSLPRGVSPQWFKGLLEQ 155
                                        **********************************************9999************************** PP

                          TIGR03828 153 lrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgvenvlislGadGallv 228
                                        l++ g+kv+lDtsgeaL+++l a p+l+KPN+eEl+e+l+++        +a+ +l+++gve+v++s Ga+G+ + 
  lcl|FitnessBrowser__WCS417:GFF781 156 LKRYGLKVALDTSGEALRAGLLAGPWLVKPNTEELAEALDNAT-------DAVSQLHRQGVEHVVVSDGAAGVSWY 224
                                        *************************************998765.......7899********************** PP

                          TIGR03828 229 tkegalfakapkievkstvGAGDsmvAgfllalekglsleealrlavAvgaaaassegtelpdledieelleevki 304
                                        ++++al+a++pk++v+stvGAGDs++Ag+l++l  g ++e++lr a+A++a a+++ g+++ d +++++l++ v++
  lcl|FitnessBrowser__WCS417:GFF781 225 SPNAALQATPPKVTVASTVGAGDSLLAGMLHGLLTGDTPEQTLRRATAIAAMAVTQIGFGISDHAQLARLESGVQV 300
                                        *************************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (305 nodes)
Target sequences:                          1  (306 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: 9.74
//
[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