Alignments for a candidate for prs in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Pseudomonas fluorescens FW300-N2E2

Align Putative ribose-phosphate pyrophosphokinase 2; RPPK 2; 5-phospho-D-ribosyl alpha-1-diphosphate synthase 2; Phosphoribosyl diphosphate synthase 2; Phosphoribosyl pyrophosphate synthase 2; P-Rib-PP synthase 2; PRPP synthase 2; PRPPase 2; EC 2.7.6.1 (characterized)
to candidate Pf6N2E2_844 Ribose-phosphate pyrophosphokinase (EC 2.7.6.1)

Query= SwissProt::Q5XC85
         (326 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_844
          Length = 330

 Score =  147 bits (371), Expect = 4e-40
 Identities = 97/304 (31%), Positives = 155/304 (50%), Gaps = 17/304 (5%)

Query: 12  LFSLTSNLPIAEKIAKAAGIPLGKMSSRQFSDGEIMINIEETVRGDDIYIIQST----SF 67
           LF+L      A ++A   G PL +   R + DGE      + V G ++ +  S       
Sbjct: 8   LFALQGCEHYAARVAHRLGCPLARHEERDYEDGEHKCRPLDPVNGREVVVFHSLYGDGRQ 67

Query: 68  PVNDNLWELLIMIDACKRASANTVNIVLPYFGYSRQDRVAKPREPITAKLVANMLTKAGI 127
             ND L  LL    A K A A  V +V PY  Y R+DR ++P++P   + VA+    +G+
Sbjct: 68  SANDKLCRLLFFCGALKDAGARQVQVVCPYLCYGRKDRRSQPQDPTITRYVASFFEASGV 127

Query: 128 DRVVTLDLH-AVQVQGFFDIPVDNLFTVPLFAERYSKLGLSGSDVVVVSPKNSGIKRARS 186
           DR++TLD+H        F +P  NL    LFAE ++   +  + VVVVSP + G KRA  
Sbjct: 128 DRLLTLDVHNPAAFDNAFRLPAWNLQCAQLFAEHFA-TQVGDAAVVVVSPDSGGTKRAEH 186

Query: 187 LAEYLDSPI------AIIDYAQDDSEREQGYIIGDVSGKKAILIDDILNTGKTFAEAAKI 240
             + L+  +      A+++  +  +      ++GDV+GK AI+ DD+++TG T   A   
Sbjct: 187 FRQALEWQLGRTVGSALMEKHRTQNTLTGSLLLGDVAGKTAIVFDDLISTGDTLKRAGLA 246

Query: 241 LERSGATDTYAVASHGLFAGGAAEVLETAPIKEIIVTDSVKTKNRVPENVT----YLSAS 296
            +++GAT  +A A+HGLF  G +++ +    + I +TD+V      P+ VT     L ++
Sbjct: 247 CQKAGATRLFAAATHGLFTTG-SQLFDPPIFERIAITDTVAPFRLPPDCVTQHLQVLDST 305

Query: 297 DLIA 300
            LIA
Sbjct: 306 GLIA 309


Lambda     K      H
   0.317    0.134    0.371 

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: 207
Number of extensions: 6
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: 326
Length of database: 330
Length adjustment: 28
Effective length of query: 298
Effective length of database: 302
Effective search space:    89996
Effective search space used:    89996
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: 49 (23.5 bits)

Align candidate Pf6N2E2_844 (Ribose-phosphate pyrophosphokinase (EC 2.7.6.1))
to HMM TIGR01251 (prs: ribose-phosphate diphosphokinase (EC 2.7.6.1))

# 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.aa/TIGR01251.hmm
# target sequence database:        /tmp/gapView.21083.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01251  [M=309]
Accession:   TIGR01251
Description: ribP_PPkin: ribose-phosphate diphosphokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
    2.9e-64  202.9   0.0    3.7e-64  202.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_844  Ribose-phosphate pyrophosphokina


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_844  Ribose-phosphate pyrophosphokinase (EC 2.7.6.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.5   0.0   3.7e-64   3.7e-64       4     295 ..       9     312 ..       7     317 .. 0.90

  Alignments for each domain:
  == domain 1  score: 202.5 bits;  conditional E-value: 3.7e-64
                                     TIGR01251   4 lsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiiv...qstsapvndal 65 
                                                   ++++  ++ a++va++lg +l + e + + dgE + r  + v+g++v+++        ++ nd+l
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_844   9 FALQGCEHYAARVAHRLGCPLARHEERDYEDGEHKCRPLDPVNGREVVVFHslyGDGRQSANDKL 73 
                                                   777888999**************************************99975554566789**** PP

                                     TIGR01251  66 mellllidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHse 130
                                                     ll+ + alk+a+a++v++v Py+ Y+R+d++ ++ +p   + va+++e+ G+dr+lt+d+H++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_844  74 CRLLFFCGALKDAGARQVQVVCPYLCYGRKDRRSQPQDPTITRYVASFFEASGVDRLLTLDVHNP 138
                                                   ****************************************************************8 PP

                                     TIGR01251 131 q.iqgfFdvpvenlsaspklieelkkke.lknlvvvsPDkGaverakkvakklglel......ai 187
                                                   +   ++F+ p+ nl+ ++ ++e+++ ++ +  +vvvsPD+G+++ra++++++l+ +l      a+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_844 139 AaFDNAFRLPAWNLQCAQLFAEHFATQVgDAAVVVVSPDSGGTKRAEHFRQALEWQLgrtvgsAL 203
                                                   62689*********************999999*******************99866544444489 PP

                                     TIGR01251 188 ieKeRdskenevevtnllgdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsg 252
                                                   +eK+R   +n+ +   llgdv+gk+++++DD+isTg Tl +a  + +++GA++ ++aathg+f+ 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_844 204 MEKHRT--QNTLTGSLLLGDVAGKTAIVFDDLISTGDTLKRAGLACQKAGATRLFAAATHGLFTT 266
                                                   ******..779****************************************************97 PP

                                     TIGR01251 253 dAlerlaeagveevivtntilv.ee...kklpkvseisvapliaeai 295
                                                    + + ++   +e++++t+t++  +      ++++++++ + lia  +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_844 267 GS-QLFDPPIFERIAITDTVAPfRLppdCVTQHLQVLDSTGLIATFL 312
                                                   65.889**************864323334556677777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (330 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: 7.76
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis