GapMind for catabolism of small carbon sources

 

Aligments for a candidate for 1pfk in Klebsiella michiganensis M5al

Align 1-phosphofructokinase (characterized)
to candidate BWI76_RS19730 BWI76_RS19730 1-phosphofructokinase

Query= CharProtDB::CH_024159
         (312 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS19730 BWI76_RS19730
           1-phosphofructokinase
          Length = 312

 Score =  606 bits (1563), Expect = e-178
 Identities = 305/312 (97%), Positives = 307/312 (98%)

Query: 1   MSRRVATITLNPAYDLVGFCPEIERGEVNLVKTTGLHAAGKGINVAKVLKDLGIDVTVGG 60
           MSRRVATITLNPAYDLVGF PEIERGEVNLV+TTGLHAAGKGINVAKVLKDLGIDVTVGG
Sbjct: 1   MSRRVATITLNPAYDLVGFTPEIERGEVNLVRTTGLHAAGKGINVAKVLKDLGIDVTVGG 60

Query: 61  FLGKDNQDGFQQLFSELGIANRFQVVQGRTRINVKLTEKDGEVTDFNFSGFEVTPADWER 120
           FLGKDNQDGFQQLFSELGIANRFQVVQGRTRINVKLTEKDGEVTDFNFSGFEVTP DWER
Sbjct: 61  FLGKDNQDGFQQLFSELGIANRFQVVQGRTRINVKLTEKDGEVTDFNFSGFEVTPGDWER 120

Query: 121 FVTDSLSWLGQFDMVCVSGSLPSGVSPEAFTDWMTRLRSQCPCIIFDSSREALVAGLKAA 180
           FV DSLSWLGQFDMVCVSGSLPSGVSPEAFTDWMTRLRSQCPCIIFDSSREALVAGLKAA
Sbjct: 121 FVNDSLSWLGQFDMVCVSGSLPSGVSPEAFTDWMTRLRSQCPCIIFDSSREALVAGLKAA 180

Query: 181 PWLVKPNRRELEIWAGRKLPEMKDVIEAAHALREQGIAHVVISLGAEGALWVNASGEWIA 240
           PWLVKPNRRELEIWAGRKLPEMKDVIEAAHALREQGIAHVVISLG EGALWVNASGEWIA
Sbjct: 181 PWLVKPNRRELEIWAGRKLPEMKDVIEAAHALREQGIAHVVISLGEEGALWVNASGEWIA 240

Query: 241 KPPSVDVVSTVGAGDSMVGGLIYGLLMRESSEHTLRLATAVAALAVSQSNVGITDRPQLA 300
           KPPSV+VVSTVGAGDSMVGGLIYGLLMRESSEHTLRLATAVAALAVSQSNVGITDR QLA
Sbjct: 241 KPPSVEVVSTVGAGDSMVGGLIYGLLMRESSEHTLRLATAVAALAVSQSNVGITDRTQLA 300

Query: 301 AMMARVDLQPFN 312
           AMMARVDLQPFN
Sbjct: 301 AMMARVDLQPFN 312


Lambda     K      H
   0.319    0.135    0.404 

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: 505
Number of extensions: 7
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: 312
Length of database: 312
Length adjustment: 27
Effective length of query: 285
Effective length of database: 285
Effective search space:    81225
Effective search space used:    81225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate BWI76_RS19730 BWI76_RS19730 (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.28522.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.7e-105  337.7   0.0     3e-105  337.5   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS19730  BWI76_RS19730 1-phosphofructokin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS19730  BWI76_RS19730 1-phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.5   0.0    3e-105    3e-105       1     304 [.       5     308 ..       5     309 .. 0.99

  Alignments for each domain:
  == domain 1  score: 337.5 bits;  conditional E-value: 3e-105
                               TIGR03828   1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeiealle 71 
                                             ++T+TlNpa+D++  + e+e+gevn v+++ l+a+GKGinVa+vLk+lg++v++ gflG+++++ +++l++
  lcl|FitnessBrowser__Koxy:BWI76_RS19730   5 VATITLNPAYDLVGFTPEIERGEVNLVRTTGLHAAGKGINVAKVLKDLGIDVTVGGFLGKDNQDGFQQLFS 75 
                                             68********************************************************************* PP

                               TIGR03828  72 eegiktdfvevkgetRinvkikessgeetklnepGpeiseeeleallekleeqlkegdvlvlaGSlPrgvp 142
                                             e gi+++f  v+g tRinvk++e++ge+t+ n++G+e+++ ++e+++++  + l + d++ ++GSlP+gv+
  lcl|FitnessBrowser__Koxy:BWI76_RS19730  76 ELGIANRFQVVQGRTRINVKLTEKDGEVTDFNFSGFEVTPGDWERFVNDSLSWLGQFDMVCVSGSLPSGVS 146
                                             *********************************************************************** PP

                               TIGR03828 143 edlyaelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgv 213
                                             ++++ +++ +lr++   +i+D+s eaL ++lka p+l+KPN++Ele ++gr+l + ++vieaa+ l+e+g+
  lcl|FitnessBrowser__Koxy:BWI76_RS19730 147 PEAFTDWMTRLRSQCPCIIFDSSREALVAGLKAAPWLVKPNRRELEIWAGRKLPEMKDVIEAAHALREQGI 217
                                             *********************************************************************** PP

                               TIGR03828 214 envlislGadGallvtkegalfakapkievkstvGAGDsmvAgfllalekglsleealrlavAvgaaaass 284
                                             ++v+islG++Gal+v+++g+++ak+p +ev+stvGAGDsmv+g++++l   +s e++lrla+Av+a a+s+
  lcl|FitnessBrowser__Koxy:BWI76_RS19730 218 AHVVISLGEEGALWVNASGEWIAKPPSVEVVSTVGAGDSMVGGLIYGLLMRESSEHTLRLATAVAALAVSQ 288
                                             *********************************************************************** PP

                               TIGR03828 285 egtelpdledieelleevki 304
                                             ++++++d+ +++++ ++v++
  lcl|FitnessBrowser__Koxy:BWI76_RS19730 289 SNVGITDRTQLAAMMARVDL 308
                                             **************999976 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: 00:00:00.01
# Mc/sec: 8.83
//
[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:

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:

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:

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