Alignments for a candidate for prs in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Phaeobacter inhibens BS107

Align Ribose-phosphate pyrophosphokinase; RPPK; 5-phospho-D-ribosyl alpha-1-diphosphate synthase; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PRPP synthase; PRPPase; EC 2.7.6.1 (characterized)
to candidate GFF2473 PGA1_c25050 ribose-phosphate pyrophosphokinase Prs

Query= SwissProt::P0A1V6
         (315 letters)



>FitnessBrowser__Phaeo:GFF2473
          Length = 339

 Score =  314 bits (805), Expect = 2e-90
 Identities = 167/319 (52%), Positives = 222/319 (69%), Gaps = 11/319 (3%)

Query: 5   KLFAGNATPELAQRIANRLYTSLG------DAAVGRFSDGEVSVQINENVRGGDIFIIQS 58
           KL AGNA   LA+ I  R+    G      DA V RF+DGE+ V++ ENVRG D+FIIQ 
Sbjct: 8   KLIAGNANLPLAETITRRMSMHRGVDQGLVDARVERFNDGEIFVEVYENVRGEDMFIIQP 67

Query: 59  TCAPTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLS 118
           T  P NDNLMEL+++ DALRR+SA RITAVIPYFGYARQDRR + AR PI+AK+VA+ L+
Sbjct: 68  TSNPANDNLMELLIIADALRRSSAQRITAVIPYFGYARQDRRTK-ARTPISAKLVANMLT 126

Query: 119 SVGVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDM---LQLNLDNPIVVSPDIGGVV 175
             G++RVLT+DLHA QIQGFFD+PVDN++ SPI   D+    + ++D  +VVSPD+GGV 
Sbjct: 127 GAGIERVLTMDLHAAQIQGFFDIPVDNLYASPIFALDVKNQFKDSMDEIMVVSPDVGGVA 186

Query: 176 RARAIAKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEA 235
           RAR +AK +N   ++I+DKRR +A     M +IGDV  + C+++DDM DT GTLCKAA+ 
Sbjct: 187 RARELAKRIN-APLSIVDKRREKAGEVAEMTVIGDVTDKICLIIDDMCDTAGTLCKAAQV 245

Query: 236 LKERGAKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGM 295
           L + GAK V AY TH + SG A   + NSV+  +V+ DTI  TD +   PN+R L  + +
Sbjct: 246 LLDNGAKEVHAYITHGVMSGPAVERVTNSVMKSLVLTDTIQPTDAVLGAPNIRILPTAPL 305

Query: 296 LAEAIRRISNEESISAMFE 314
             +AI  I +  S+S++FE
Sbjct: 306 FTQAILNIWHGTSVSSLFE 324


Lambda     K      H
   0.322    0.137    0.386 

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: 305
Number of extensions: 11
Number of successful extensions: 4
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: 315
Length of database: 339
Length adjustment: 28
Effective length of query: 287
Effective length of database: 311
Effective search space:    89257
Effective search space used:    89257
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate GFF2473 PGA1_c25050 (ribose-phosphate pyrophosphokinase Prs)
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.24304.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   4.3e-111  356.7   0.2   4.9e-111  356.5   0.2    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2473  PGA1_c25050 ribose-phosphate pyr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2473  PGA1_c25050 ribose-phosphate pyrophosphokinase Prs
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.5   0.2  4.9e-111  4.9e-111       3     309 .]       9     324 ..       7     324 .. 0.94

  Alignments for each domain:
  == domain 1  score: 356.5 bits;  conditional E-value: 4.9e-111
                          TIGR01251   3 ilsgssskelaekvaknlgle......lgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelllli 72 
                                        +++g+++  lae + ++++++      l+d++v++F dgE+ v++ e+vrg+d+fii q ts+p nd+lmell+++
  lcl|FitnessBrowser__Phaeo:GFF2473   9 LIAGNANLPLAETITRRMSMHrgvdqgLVDARVERFNDGEIFVEVYENVRGEDMFII-QPTSNPANDNLMELLIIA 83 
                                        677888888888887776654333333899***************************.****************** PP

                          TIGR01251  73 dalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspk 148
                                        dal+r+sa+++taviPy+gYaRqd+++k r+pisaklva++l+ aG++rvlt+dlH+ qiqgfFd+pv+nl+asp 
  lcl|FitnessBrowser__Phaeo:GFF2473  84 DALRRSSAQRITAVIPYFGYARQDRRTKARTPISAKLVANMLTGAGIERVLTMDLHAAQIQGFFDIPVDNLYASPI 159
                                        **************************************************************************** PP

                          TIGR01251 149 lieelkkke...lknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDDiis 221
                                        ++ ++k++    +++++vvsPD G+v+ra+++ak+++++l+i++K+R+ k+ ev  + ++gdv +k ++i+DD+ +
  lcl|FitnessBrowser__Phaeo:GFF2473 160 FALDVKNQFkdsMDEIMVVSPDVGGVARARELAKRINAPLSIVDKRRE-KAGEVAEMTVIGDVTDKICLIIDDMCD 234
                                        ****99988888999*********************************.667************************ PP

                          TIGR01251 222 TggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kklpkvseisvapliaeai 295
                                        T+gTl+kaa++L ++GAk+v +++thgv+sg+A+er+++++++ ++ t+ti+  +     p+++ +  apl+ +ai
  lcl|FitnessBrowser__Phaeo:GFF2473 235 TAGTLCKAAQVLLDNGAKEVHAYITHGVMSGPAVERVTNSVMKSLVLTDTIQPtDAvLGAPNIRILPTAPLFTQAI 310
                                        ***************************************************995557889**************** PP

                          TIGR01251 296 arihenesvsslfd 309
                                        ++i +++svsslf+
  lcl|FitnessBrowser__Phaeo:GFF2473 311 LNIWHGTSVSSLFE 324
                                        ************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (339 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: 8.23
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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