GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prs in Dyella japonica UNC79MFTsu3.2

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 N515DRAFT_2463 N515DRAFT_2463 ribose-phosphate pyrophosphokinase

Query= curated2:Q8TUT6
         (291 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2463
          Length = 293

 Score =  127 bits (319), Expect = 3e-34
 Identities = 90/290 (31%), Positives = 143/290 (49%), Gaps = 8/290 (2%)

Query: 2   IVLATSEGVKLGRRLAEELDAELAPVEEDRFPDGEQIVRV-PPELDGTVVVVHSMSPPQD 60
           +V A     +L   LA         +E  RFPDGE +VRV  P +    ++V ++  P D
Sbjct: 4   VVYAMPGNQELADALAHRRRMARLALELHRFPDGEGLVRVEEPPVGAEAIIVCTLDRP-D 62

Query: 61  ENLVKAIITLDAARENGAEEVIAIVPYMAYSRQDRRFEPGEPVSFRAVARAVSANADALI 120
           E  +  ++  D  RE GA  V  + PY+AY RQD RF PGE VS     R ++ + D  +
Sbjct: 63  EKTLPLLMAADTLRELGAGSVGLVAPYLAYLRQDARFRPGEAVSSGIFGRLLAEHFDWQV 122

Query: 121 TVD--LHEPGTLKYFDVP-AENVSAAEELGKYLAERFEGEDLVVIGPDEGARELAREVAS 177
           T+D  LH   +L    +P    +SAA  L  +L ER E    ++IGPDE +      VA+
Sbjct: 123 TIDPHLHRLRSLTEAGMPQGRAISAAPALAGWLRERVELP--LLIGPDEESAPWVESVAA 180

Query: 178 ICGVEYDHLEKKRLSGDEVEIHPKEL-DVEGRTVVLVDDMIDTGGTMVEAARALRDQGAG 236
           +         K+R    +V++   +L +  G   VL+DD+I +G T++++   LR  G  
Sbjct: 181 LMSAPAVVATKRRFGDRKVQVQLPDLSNWPGHNPVLLDDIISSGHTLLKSIEGLRALGMP 240

Query: 237 TLYAACTHALLTRNAATRLLASGFEDIIATDTVPNPFEKVSVAPPVAEAV 286
             +    H L   NA  RL  +G   ++ T++VP    ++ ++  +A A+
Sbjct: 241 APWCVAVHGLFADNALERLRVAGVAGVVTTNSVPGETARIDLSELLAAAL 290


Lambda     K      H
   0.314    0.134    0.370 

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: 178
Number of extensions: 8
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: 291
Length of database: 293
Length adjustment: 26
Effective length of query: 265
Effective length of database: 267
Effective search space:    70755
Effective search space used:    70755
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: 42 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate N515DRAFT_2463 N515DRAFT_2463 (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.1162398.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    4.7e-52  162.8   0.0    5.3e-52  162.6   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2463  N515DRAFT_2463 ribose-phosphate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2463  N515DRAFT_2463 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.6   0.0   5.3e-52   5.3e-52       5     295 ..       7     290 ..       3     293 .] 0.93

  Alignments for each domain:
  == domain 1  score: 162.6 bits;  conditional E-value: 5.3e-52
                                    TIGR01251   5 sgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelll 70 
                                                  + + ++ela+++a++  +  +  e ++F+dgE  vr+ee   g + +i+   t    +++ + ll+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2463   7 AMPGNQELADALAHRRRMARLALELHRFPDGEGLVRVEEPPVGAEAIIV--CTLDRPDEKTLPLLM 70 
                                                  56789**************************************999999..677789********* PP

                                    TIGR01251  71 lidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfF 136
                                                  ++d+l++ +a+sv +v+Py++Y Rqd +++++e++s+ ++++ll+e   d  +t+d H + +++  
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2463  71 AADTLRELGAGSVGLVAPYLAYLRQDARFRPGEAVSSGIFGRLLAEH-FDWQVTIDPHLHRLRSLT 135
                                                  ***********************************************.************999999 PP

                                    TIGR01251 137 d...vpvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenev 199
                                                  +    + + +sa+p l+ +l+++ ++ ++++ PD+ ++ ++++va+ + ++ ++  K+R  ++ +v
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2463 136 EagmPQGRAISAAPALAGWLRER-VELPLLIGPDEESAPWVESVAALMSAPAVVATKRRFGDR-KV 199
                                                  843124477999*********97.9999********************************555.77 PP

                                    TIGR01251 200 evt.nllgdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagve 264
                                                  +v+ + l +  g + v++DDiis+g+Tl+k++e L+  G     ++a+hg+f+++Alerl+ agv 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2463 200 QVQlPDLSNWPGHNPVLLDDIISSGHTLLKSIEGLRALGMPAPWCVAVHGLFADNALERLRVAGVA 265
                                                  7762556799******************************************************** PP

                                    TIGR01251 265 evivtntilveekklpkvseisvapliaeai 295
                                                   v+ tn+++       +  +i++++l+a a+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2463 266 GVVTTNSVPG------ETARIDLSELLAAAL 290
                                                  **********......889999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (293 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: 20.51
//
[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:

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:

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:

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:

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