Alignments for a candidate for prs in Pseudomonas fluorescens FW300-N2E3

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Pseudomonas fluorescens FW300-N2E3

Align Ribose-phosphate pyrophosphokinase; RPPK; EC 2.7.6.1; 5-phospho-D-ribosyl alpha-1-diphosphate synthase; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PRPP synthase; PRPPase (uncharacterized)
to candidate AO353_19995 AO353_19995 ribose-phosphate pyrophosphokinase

Query= curated2:Q8RHM2
         (316 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_19995
          Length = 321

 Score =  158 bits (400), Expect = 1e-43
 Identities = 96/282 (34%), Positives = 160/282 (56%), Gaps = 16/282 (5%)

Query: 9   IFSGNSNLELAKKIAEKAGLQLGKAEIQRFKDGEVYIEIEETVRGRDVFVVQST----SE 64
           +F+   +   A ++A++ G QL + E + ++DGE      E+V GR+V V  S      +
Sbjct: 8   LFALQGSEHYASRVAQRLGCQLARHEERDYEDGEHKCRPLESVNGREVVVFHSLYGDDRQ 67

Query: 65  PVNENLMELLIFVDALKRASAKTINVIIPYYGYARQDRKSKPREPITSKLVANLLTTAGV 124
             N+ L  LL F  ALK A A+ +  + PY  Y R+DR+++P++P  ++ VA ++   GV
Sbjct: 68  SANDKLCRLLFFCGALKDAGARQVQAVTPYLCYGRKDRRTQPQDPTITRYVAAMIEACGV 127

Query: 125 NRVVAMDLH-ADQIQGFFDIPLDHMQALPLMARYFKEKGFKGD-EVVVVSPDVGGVKRAR 182
           +R+VA+++H        F IP  ++Q   L AR+F   GF GD EVV VSPD GG KRA 
Sbjct: 128 DRLVALEVHNPAAFDNAFRIPTWNVQCAELFARHF--AGFVGDAEVVSVSPDAGGTKRAE 185

Query: 183 KLAEKLDCKI------AIIDKRRPKPNMSEVMNLIGEVEGKIAIFIDDMIDTAGTITNGA 236
           +  + L+ ++      A+++K R +   +  + L+GEV GK AI  DD+I T  T+ +  
Sbjct: 186 QFRQALERQLGRVVGGALMEKHRAQATFTGTL-LVGEVLGKTAIIFDDLISTGETLMHAG 244

Query: 237 DAIAQRGAKEVYACCTHAVFSDPAIERLEKSVLKEIVITDSI 278
            A  Q GA  ++A  TH +F+  + + L+K + + + ++DS+
Sbjct: 245 LACQQAGATRLFAAATHGLFTGGS-DLLDKPLFEHLAVSDSV 285


Lambda     K      H
   0.319    0.136    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: 170
Number of extensions: 5
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: 321
Length adjustment: 27
Effective length of query: 289
Effective length of database: 294
Effective search space:    84966
Effective search space used:    84966
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate AO353_19995 AO353_19995 (ribose-phosphate pyrophosphokinase)
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.11763.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
    2.5e-62  196.5   0.0    3.2e-62  196.2   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_19995  AO353_19995 ribose-phosphate pyr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_19995  AO353_19995 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.2   0.0   3.2e-62   3.2e-62       3     294 ..       8     311 ..       7     318 .. 0.89

  Alignments for each domain:
  == domain 1  score: 196.2 bits;  conditional E-value: 3.2e-62
                                     TIGR01251   3 ilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiiv...qstsapvnda 64 
                                                   +++++ s++ a++va++lg +l + e + + dgE + r  esv+g++v+++        ++ nd+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_19995   8 LFALQGSEHYASRVAQRLGCQLARHEERDYEDGEHKCRPLESVNGREVVVFHslyGDDRQSANDK 72 
                                                   5889999*****************************************99975553445679*** PP

                                     TIGR01251  65 lmellllidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHs 129
                                                   l  ll+ + alk+a+a++v+av Py+ Y+R+d+++++ +p   + va ++e+ G+dr++++++H+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_19995  73 LCRLLFFCGALKDAGARQVQAVTPYLCYGRKDRRTQPQDPTITRYVAAMIEACGVDRLVALEVHN 137
                                                   ***************************************************************** PP

                                     TIGR01251 130 eq.iqgfFdvpvenlsaspklieelkkke.lknlvvvsPDkGaverakkvakklglel......a 186
                                                   ++   ++F++p  n++ ++ ++++++  + + ++v vsPD+G+++ra++++++l+ +l      a
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_19995 138 PAaFDNAFRIPTWNVQCAELFARHFAGFVgDAEVVSVSPDAGGTKRAEQFRQALERQLgrvvggA 202
                                                   862689********************9999999999****************9997765555558 PP

                                     TIGR01251 187 iieKeRdskenevevtnllgdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfs 251
                                                   ++eK+R  ++ + + t l+g+v gk+++i+DD+isTg Tl++a  + +++GA++ ++aathg+f+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_19995 203 LMEKHRA-QA-TFTGTLLVGEVLGKTAIIFDDLISTGETLMHAGLACQQAGATRLFAAATHGLFT 265
                                                   9******.33.79**************************************************** PP

                                     TIGR01251 252 gdAlerlaeagveevivtntilv.ee...kklpkvseisvapliaea 294
                                                   g +   l++  +e+++v+++++  +       +++++++ + lia  
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_19995 266 GGS-DLLDKPLFEHLAVSDSVPPfRLppdCVAHRLHVLDSTALIATL 311
                                                   986.789**************86332322344556666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (321 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: 7.16
//
[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