Alignments for a candidate for prs in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Cupriavidus basilensis 4G11

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 RR42_RS11675 RR42_RS11675 phosphoribosylpyrophosphate synthetase

Query= curated2:Q8TUT6
         (291 letters)



>FitnessBrowser__Cup4G11:RR42_RS11675
          Length = 298

 Score =  137 bits (345), Expect = 3e-37
 Identities = 100/280 (35%), Positives = 138/280 (49%), Gaps = 7/280 (2%)

Query: 11  KLGRRLAEELDAELAPVEEDRFPDGEQIVRVPPELDGTVVVVHSMSPPQDENLVKAIITL 70
           +  R LA  L A+        F DGE  VR+   L G   ++       DE +V  +   
Sbjct: 13  RAARALASALGADWGSAAIRHFADGESSVRLLSPLQGRQAILFCTLDRPDEKIVPLLWAA 72

Query: 71  DAARENGAEEVIAIVPYMAYSRQDRRFEPGEPVSFRAVARAVSANADALITVD--LHEPG 128
            AARE+GA  V  + PY+AY RQD  F PGE V+ R  A  +S + D L+TVD  LH   
Sbjct: 73  IAARESGASRVGLVAPYLAYMRQDAVFHPGEIVAARHFAALLSRHFDWLVTVDPHLHRIA 132

Query: 129 TL-KYFDVPAENVSAAEELGKYLAERFEGEDLVVIGPDEGARELAREVASICGVEYDHLE 187
           TL   + +P + V AA  +  +L  R       ++GPDE +R+   +VA  C      L 
Sbjct: 133 TLDDIYTIPTQCVQAAPAIASWL--RATVNQPFLVGPDEESRQWVNDVARRCQAPAIVLH 190

Query: 188 KKRLSGDEVEIHPKELD-VEGRTVVLVDDMIDTGGTMVEAARALRDQGAGTLYAACTHAL 246
           K R +   VEI   +L+   G T VL+DD++ TG TMV AA  LR  G         HA+
Sbjct: 191 KTRHADRCVEIQAADLNAAAGCTPVLLDDIVATGSTMVAAANLLRRAGLAPPVCVAVHAV 250

Query: 247 LTRNAATRLLASGFEDIIATDTVPNPFEKVSVAPPVAEAV 286
              +A   L A   E I+  DTV +    +++A P+AEAV
Sbjct: 251 FAGDAFAELRAVAAE-IVTCDTVSHSSNGIALAAPLAEAV 289


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: 172
Number of extensions: 7
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: 298
Length adjustment: 26
Effective length of query: 265
Effective length of database: 272
Effective search space:    72080
Effective search space used:    72080
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 RR42_RS11675 RR42_RS11675 (phosphoribosylpyrophosphate synthetase)
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.9543.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.3e-55  174.5   0.0    1.6e-55  174.2   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS11675  RR42_RS11675 phosphoribosylpyrop


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS11675  RR42_RS11675 phosphoribosylpyrophosphate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.2   0.0   1.6e-55   1.6e-55       3     298 ..       5     292 ..       4     297 .. 0.91

  Alignments for each domain:
  == domain 1  score: 174.2 bits;  conditional E-value: 1.6e-55
                                 TIGR01251   3 ilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellll 71 
                                               +++++ +++ a+++a +lg + g++ +++FadgE +vr+ + ++g++ +++   t    +++++ ll +
  lcl|FitnessBrowser__Cup4G11:RR42_RS11675   5 LFALPGNERAARALASALGADWGSAAIRHFADGESSVRLLSPLQGRQAILF--CTLDRPDEKIVPLLWA 71 
                                               5778889999***********************************777777..677789********** PP

                                 TIGR01251  72 idalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiq...gfFd 137
                                               + a+++++a++v +v+Py++Y Rqd  ++++e ++a+ +a ll+    d ++tvd H + i    ++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS11675  72 AIAARESGASRVGLVAPYLAYMRQDAVFHPGEIVAARHFAALLSRH-FDWLVTVDPHLHRIAtldDIYT 139
                                               **********************************************.**********998853337899 PP

                                 TIGR01251 138 vpvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllg 206
                                               +p + ++a+p ++ +l+++ ++++ +v PD+ + +++++va++ +++  +++K+R+ ++  ve+++ ++
  lcl|FitnessBrowser__Cup4G11:RR42_RS11675 140 IPTQCVQAAPAIASWLRAT-VNQPFLVGPDEESRQWVNDVARRCQAPAIVLHKTRH-ADRCVEIQAADL 206
                                               *****************96.999999******************************.6669***99999 PP

                                 TIGR01251 207 dv.egkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv 274
                                               +  +g + v++DDi++Tg T+v+aa+lL+++G    +++a+h+vf+gdA   l+   + e++ ++t+ +
  lcl|FitnessBrowser__Cup4G11:RR42_RS11675 207 NAaAGCTPVLLDDIVATGSTMVAAANLLRRAGLAPPVCVAVHAVFAGDAFAELRAV-AAEIVTCDTVSH 274
                                               862799**************************9999999**************876.99********** PP

                                 TIGR01251 275 eekklpkvseisvapliaeaiari 298
                                                       + i +a  +aea++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS11675 275 ------SSNGIALAAPLAEAVSAV 292
                                               ......556666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (298 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: 00:00:00.01
# Mc/sec: 8.20
//
[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