GapMind for catabolism of small carbon sources

 

Alignments for a candidate for 1pfk in Catellicoccus marimammalium M35/04/3

Align 1-phosphofructokinase; EC 2.7.1.56; Fructose 1-phosphate kinase (uncharacterized)
to candidate WP_009489922.1 C683_RS03170 1-phosphofructokinase

Query= curated2:O31714
         (303 letters)



>NCBI__GCF_000313915.1:WP_009489922.1
          Length = 304

 Score =  283 bits (725), Expect = 3e-81
 Identities = 139/303 (45%), Positives = 203/303 (66%)

Query: 1   MIYTVTLNPSVDYIVHVEDFTVGGLNRSSYDTKYPGGKGINVSRLLKRHHVASKALGFVG 60
           MIYT+TLNPS+DY++ ++   +G +NR   D K+PGGKGINVSR+L+R  + + ALG+VG
Sbjct: 1   MIYTITLNPSIDYVIQMDHLELGTVNRMDTDFKFPGGKGINVSRILQRLEIPNTALGYVG 60

Query: 61  GFTGEYIKTFLREENLETAFSEVKGDTRINVKLKTGDETEINGQGPTISDEDFKAFLEQF 120
           GFTG +I   L +EN+ T F  +  DTRINVK+K   ETEING GP IS+ + +   +Q 
Sbjct: 61  GFTGAFITNELAKENITTDFISIAEDTRINVKIKAQQETEINGAGPMISEAEQQQLFDQL 120

Query: 121 QSLQEGDIVVLAGSIPSSLPHDTYEKIAEACKQQNARVVLDISGEALLKATEMKPFLMKP 180
             + + DI+V AGS P +L    Y+K+ +   ++ A+ V+D +G+ L  A   +P ++KP
Sbjct: 121 SQVTKEDIIVFAGSTPKNLKDGFYQKLIQFVTERGAQFVIDTTGKDLEAALSFRPLVVKP 180

Query: 181 NHHELGEMFGTAITSVEEAVPYGKKLVEQGAEHVIVSMAGDGALLFTNEAVYFANVPKGK 240
           N  EL E++ T   + E+  PY +KL+ +GA+ V++SMAGDGALLF  E +YFA   K  
Sbjct: 181 NKDELAELYQTTFETQEDIYPYAQKLMAEGAQQVLISMAGDGALLFEGENIYFAAPLKKP 240

Query: 241 LVNSVGAGDSVVAGFLAGISKQLPLEEAFRLGVTSGSATAFSEELGTEEFVQQLLPEVKV 300
           L NSVGAGDS++AGF    ++     EAF++GV  GSATAFS++L T +F+Q+   EV +
Sbjct: 241 LKNSVGAGDSMIAGFTGTYAQTKNPLEAFKMGVACGSATAFSDDLATADFIQECYNEVVI 300

Query: 301 TRL 303
            ++
Sbjct: 301 EKI 303


Lambda     K      H
   0.315    0.134    0.372 

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: 270
Number of extensions: 8
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: 303
Length of database: 304
Length adjustment: 27
Effective length of query: 276
Effective length of database: 277
Effective search space:    76452
Effective search space used:    76452
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: 42 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate WP_009489922.1 C683_RS03170 (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.2375065.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.5e-113  363.0   0.1   6.2e-113  362.8   0.1    1.0  1  NCBI__GCF_000313915.1:WP_009489922.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000313915.1:WP_009489922.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.8   0.1  6.2e-113  6.2e-113       1     305 []       2     301 ..       2     301 .. 0.99

  Alignments for each domain:
  == domain 1  score: 362.8 bits;  conditional E-value: 6.2e-113
                             TIGR03828   1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeiealleee 73 
                                           I+T+TlNp+iD++i++++lelg+vnr+ ++ +++gGKGinV+r+L++l+++++alg++Ggftg++i+++l++e
  NCBI__GCF_000313915.1:WP_009489922.1   2 IYTITLNPSIDYVIQMDHLELGTVNRMDTDFKFPGGKGINVSRILQRLEIPNTALGYVGGFTGAFITNELAKE 74 
                                           9************************************************************************ PP

                             TIGR03828  74 giktdfvevkgetRinvkikessgeetklnepGpeiseeeleallekleeqlkegdvlvlaGSlPrgvpedly 146
                                           +i+tdf+ ++++tRinvkik  +++et++n++Gp ise+e+++l+++l+ q++++d++v+aGS P+++++ +y
  NCBI__GCF_000313915.1:WP_009489922.1  75 NITTDFISIAEDTRINVKIK--AQQETEINGAGPMISEAEQQQLFDQLS-QVTKEDIIVFAGSTPKNLKDGFY 144
                                           ********************..8**************************.9********************** PP

                             TIGR03828 147 aelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgvenvlis 219
                                           ++li+ + e+ga++++Dt+g+ L ++l+++pl++KPNk+El+el +++++t+e++  +a+kl+++g+++vlis
  NCBI__GCF_000313915.1:WP_009489922.1 145 QKLIQFVTERGAQFVIDTTGKDLEAALSFRPLVVKPNKDELAELYQTTFETQEDIYPYAQKLMAEGAQQVLIS 217
                                           ************************************************************************* PP

                             TIGR03828 220 lGadGallvtkegalfakapkievkstvGAGDsmvAgfllalekglsleealrlavAvgaaaassegtelpdl 292
                                           +++dGall++ e+ +fa + k  +k++vGAGDsm+Agf+ ++++++++ ea++++vA+g+a+a+s++  l++ 
  NCBI__GCF_000313915.1:WP_009489922.1 218 MAGDGALLFEGENIYFAAPLKKPLKNSVGAGDSMIAGFTGTYAQTKNPLEAFKMGVACGSATAFSDD--LATA 288
                                           *******************************************************************..**** PP

                             TIGR03828 293 edieelleevkie 305
                                           + i+e+++ev ie
  NCBI__GCF_000313915.1:WP_009489922.1 289 DFIQECYNEVVIE 301
                                           **********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (305 nodes)
Target sequences:                          1  (304 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: 00:00:00.00
# Mc/sec: 14.04
//
[ok]

This GapMind analysis is from Sep 24 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:

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