Alignments for a candidate for 1pfk in Phaeacidiphilus oryzae TH49

GapMind for catabolism of small carbon sources

Alignments for a candidate for 1pfk in Phaeacidiphilus oryzae TH49

Align 1-phosphofructokinase; EC 2.7.1.56; Fructose 1-phosphate kinase (uncharacterized)
to candidate WP_037577290.1 BS73_RS28555 1-phosphofructokinase

Query= curated2:P23386
         (316 letters)



>NCBI__GCF_000744815.1:WP_037577290.1
          Length = 331

 Score =  171 bits (434), Expect = 2e-47
 Identities = 120/321 (37%), Positives = 155/321 (48%), Gaps = 11/321 (3%)

Query: 4   RIATVSLNSAVDQTVTVPG---FTADAVNRVAASRIDAGGKGVNVASFLAHVGHGVAVTG 60
           RI TV+ N ++D+T  +P         VNR A  R+D GGKGVNV+  L   GH      
Sbjct: 7   RIVTVTPNPSLDRTYELPAPAPLVRGGVNRAAGDRLDPGGKGVNVSRALTAAGHATRAVL 66

Query: 61  LLGAENAALFARHFAATGLVDACQRLPGATRTNVKIVDPLQDQVTDLNFPGIAAGPADLD 120
            LG     L     A  G+      + G TR NV + +P    +T +N PG    PA+  
Sbjct: 67  PLGGPGGRLLGELLAEQGIEVRAVPVRGGTRINVGVAEP-GGPLTKINAPGPELTPAESA 125

Query: 121 AVAATLTELLAQGLDWVALCGSLPAGIGAEAYAELAALARKGGARVALDTSGPALGLALA 180
           A+ A + +    G  W+A CGSLP G+  + YA   A     GAR+ALDTSGPAL  ALA
Sbjct: 126 ALLAEVRDSARAGTGWLACCGSLPRGLPDDWYARAVAAVHGAGARIALDTSGPALAAALA 185

Query: 181 ARPDIVKPNVAELGAHLGRTLTGLESVREAARDLAASGVGLVAVSMGAGGAVLVRGAEAV 240
           A PD++KPN+ EL   +G  L  L    +AA++L   G   V  S+GA G +LV      
Sbjct: 186 AGPDVLKPNLDELAEAVGGELRTLGDAVDAAKELRKRGAVAVLASLGARGMLLVAEDGCW 245

Query: 241 LAIPPATP--IASTVGAGDAMVAGLIHAATLG---LDLAETARLATAFSLGALGE--IGP 293
               P  P  + S VGAGDA +AG + A   G      A  A LA A + GA      G 
Sbjct: 246 YGTAPVDPAEVRSDVGAGDASLAGFLGAGGAGGAAGGAAGPAALAAALAHGAAAVRLPGS 305

Query: 294 HLPPPERLAALARTVTVKTLP 314
            +P P  L     TVT    P
Sbjct: 306 AMPRPSDLRPQDVTVTPDLSP 326


Lambda     K      H
   0.318    0.133    0.377 

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: 351
Number of extensions: 23
Number of successful extensions: 3
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: 316
Length of database: 331
Length adjustment: 28
Effective length of query: 288
Effective length of database: 303
Effective search space:    87264
Effective search space used:    87264
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 WP_037577290.1 BS73_RS28555 (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.736839.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.6e-92  295.1   0.0    3.1e-92  294.8   0.0    1.0  1  NCBI__GCF_000744815.1:WP_037577290.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037577290.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.8   0.0   3.1e-92   3.1e-92       1     297 [.       8     315 ..       8     321 .. 0.93

  Alignments for each domain:
  == domain 1  score: 294.8 bits;  conditional E-value: 3.1e-92
                             TIGR03828   1 IlTvTlNpaiDktielee...lelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeieall 70 
                                           I+TvT+Np++D+t+el     l +g vnr++ +rld+gGKG+nV+r+L+++g+ + a+++lGg  g+ + +ll
  NCBI__GCF_000744815.1:WP_037577290.1   8 IVTVTPNPSLDRTYELPApapLVRGGVNRAAGDRLDPGGKGVNVSRALTAAGHATRAVLPLGGPGGRLLGELL 80 
                                           99**************86222667************************************************* PP

                             TIGR03828  71 eeegiktdfvevkgetRinvkikessgeetklnepGpeiseeeleallekleeqlkegd.vlvlaGSlPrgvp 142
                                           +e+gi+++ v v+g tRinv ++e+ g  tk+n+pGpe++++e +all+++++ +++g+ +l ++GSlPrg+p
  NCBI__GCF_000744815.1:WP_037577290.1  81 AEQGIEVRAVPVRGGTRINVGVAEPGGPLTKINAPGPELTPAESAALLAEVRDSARAGTgWLACCGSLPRGLP 153
                                           ****************************************************99965544************* PP

                             TIGR03828 143 edlyaelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgven 215
                                           +d+ya+ +++++ +ga+++lDtsg+aL+++l+a p+++KPN +El+e++g el t +++++aa++l+++g+ +
  NCBI__GCF_000744815.1:WP_037577290.1 154 DDWYARAVAAVHGAGARIALDTSGPALAAALAAGPDVLKPNLDELAEAVGGELRTLGDAVDAAKELRKRGAVA 226
                                           ************************************************************************* PP

                             TIGR03828 216 vlislGadGallvtkegalfakap..kievkstvGAGDsmvAgflla.....lekglsleealrlavAvgaaa 281
                                           vl+slGa+G+llv ++g ++++ap    ev+s+vGAGD+++Agfl a      + g+   +al+ a+A+gaaa
  NCBI__GCF_000744815.1:WP_037577290.1 227 VLASLGARGMLLVAEDGCWYGTAPvdPAEVRSDVGAGDASLAGFLGAggaggAAGGAAGPAALAAALAHGAAA 299
                                           ***********************722578***************9762222255666777************* PP

                             TIGR03828 282 assegtelpdlediee 297
                                           +  +g+++p ++d+  
  NCBI__GCF_000744815.1:WP_037577290.1 300 VRLPGSAMPRPSDLRP 315
                                           ************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (305 nodes)
Target sequences:                          1  (331 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: 21.04
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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