Alignments for a candidate for prs in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Dinoroseobacter shibae DFL-12

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 3609547 Dshi_2931 ribose-phosphate pyrophosphokinase (RefSeq)

Query= SwissProt::P0A1V6
         (315 letters)



>FitnessBrowser__Dino:3609547
          Length = 340

 Score =  314 bits (804), Expect = 2e-90
 Identities = 164/319 (51%), Positives = 222/319 (69%), Gaps = 11/319 (3%)

Query: 5   KLFAGNATPELAQRIANRLYTSLG------DAAVGRFSDGEVSVQINENVRGGDIFIIQS 58
           K+ +GNA  ELA  I+ R+    G      DA V RF+DGE+ V++ ENVRG D+FIIQS
Sbjct: 8   KIISGNANQELAHAISRRMSAYRGMTVGLVDARVERFNDGEIFVEVFENVRGEDMFIIQS 67

Query: 59  TCAPTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLS 118
           T  P NDNLMEL++M DALRR+SA RITA+IPYFGYARQDRR + AR PITAK+VA+ + 
Sbjct: 68  TSNPANDNLMELLIMCDALRRSSAARITAIIPYFGYARQDRRTK-ARTPITAKLVANMMV 126

Query: 119 SVGVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQL---NLDNPIVVSPDIGGVV 175
             G++RVLT+DLHA QIQGFFD+PVDN++ +PI   D++      LDN  VVSPD+GGV 
Sbjct: 127 EAGIERVLTMDLHAAQIQGFFDIPVDNLYAAPIFALDVMHNFAGRLDNVTVVSPDVGGVA 186

Query: 176 RARAIAKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEA 235
           RAR +A+ +    +AI+DKRR +  V + M +IG+V G+ C++VDD+ DT GTLCKAA+ 
Sbjct: 187 RARELAQRIG-CGLAIVDKRRSQPGVVEEMTVIGEVEGQTCIIVDDICDTAGTLCKAADL 245

Query: 236 LKERGAKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGM 295
           L   GA  V +Y TH + SG A   +  S +  +V+ D+I  TD +KA PN+R +  + +
Sbjct: 246 LISEGASEVHSYITHGVLSGPAVERITKSNMKSLVITDSIGATDAVKAAPNIRIVPTAPV 305

Query: 296 LAEAIRRISNEESISAMFE 314
            A+AI  I N  S+S++F+
Sbjct: 306 FAQAILNIWNGTSVSSLFD 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: 316
Number of extensions: 25
Number of successful extensions: 5
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: 340
Length adjustment: 28
Effective length of query: 287
Effective length of database: 312
Effective search space:    89544
Effective search space used:    89544
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 3609547 Dshi_2931 (ribose-phosphate pyrophosphokinase (RefSeq))
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.22384.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.8e-114  365.9   0.4   7.9e-114  365.7   0.4    1.0  1  lcl|FitnessBrowser__Dino:3609547  Dshi_2931 ribose-phosphate pyrop


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609547  Dshi_2931 ribose-phosphate pyrophosphokinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  365.7   0.4  7.9e-114  7.9e-114       2     309 .]       8     324 ..       7     324 .. 0.96

  Alignments for each domain:
  == domain 1  score: 365.7 bits;  conditional E-value: 7.9e-114
                         TIGR01251   2 kilsgssskelaekvaknlg......lelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelllli 72 
                                       ki+sg++++ela++++++++      + l+d++v++F dgE+ v++ e+vrg+d+fii qsts+p nd+lmell+++
  lcl|FitnessBrowser__Dino:3609547   8 KIISGNANQELAHAISRRMSayrgmtVGLVDARVERFNDGEIFVEVFENVRGEDMFII-QSTSNPANDNLMELLIMC 83 
                                       799*********9998875422222257899***************************.****************** PP

                         TIGR01251  73 dalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspkl 149
                                       dal+r+sa ++ta+iPy+gYaRqd+++k r+pi+aklva+++ eaG++rvlt+dlH+ qiqgfFd+pv+nl+a+p +
  lcl|FitnessBrowser__Dino:3609547  84 DALRRSSAARITAIIPYFGYARQDRRTKARTPITAKLVANMMVEAGIERVLTMDLHAAQIQGFFDIPVDNLYAAPIF 160
                                       ***************************************************************************** PP

                         TIGR01251 150 ieelkkke...lknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDDiisTg 223
                                       + ++ ++    l+n++vvsPD G+v+ra+++a+++g+ lai++K+R  +  +ve + ++g+veg++++ivDDi +T+
  lcl|FitnessBrowser__Dino:3609547 161 ALDVMHNFagrLDNVTVVSPDVGGVARARELAQRIGCGLAIVDKRRS-QPGVVEEMTVIGEVEGQTCIIVDDICDTA 236
                                       *****999999************************************.666************************** PP

                         TIGR01251 224 gTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kklpkvseisvapliaeaiari 298
                                       gTl+kaa+lL ++GA++v  ++thgv+sg+A+er++++ ++ +++t++i   +  k+ p+++ +  ap++a+ai++i
  lcl|FitnessBrowser__Dino:3609547 237 GTLCKAADLLISEGASEVHSYITHGVLSGPAVERITKSNMKSLVITDSIGAtDAvKAAPNIRIVPTAPVFAQAILNI 313
                                       ***************************************************5559********************** PP

                         TIGR01251 299 henesvsslfd 309
                                        +++svsslfd
  lcl|FitnessBrowser__Dino:3609547 314 WNGTSVSSLFD 324
                                       *********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (340 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 12.12
//
[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