Alignments for a candidate for prs in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Pseudomonas stutzeri RCH2

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 GFF3459 Psest_3524 ribose-phosphate pyrophosphokinase

Query= curated2:Q8TUT6
         (291 letters)



>FitnessBrowser__psRCH2:GFF3459
          Length = 298

 Score =  144 bits (362), Expect = 3e-39
 Identities = 102/284 (35%), Positives = 149/284 (52%), Gaps = 13/284 (4%)

Query: 15  RLAEELDAELAPVEEDRFPDGEQIVRVPPELDGTVV----VVHSMSPPQDENLVKAIITL 70
           RLAE      A +E  RFPD E  +R+P   DG  +    V++      +E LV+ ++  
Sbjct: 17  RLAEACGLTAAQIERHRFPDDELRLRLPLA-DGEAIAEQLVIYRGLDHPNEKLVELLLIA 75

Query: 71  DAARENGAEEVIAIVPYMAYSRQDRRFEPGEPVSFRAVARAVSANADALITVD--LHEPG 128
             AR  GA+ ++ + PY+AY RQD  F PGE VS R + + ++   D LITVD  LH   
Sbjct: 76  GEARRLGAKRLVLVTPYLAYMRQDIAFNPGEVVSQRVIGQLLAGQFDGLITVDPHLHRVA 135

Query: 129 TLKYFDVPAEN---VSAAEELGKYLAERFEGEDLVVIGPDEGARELAREVASICGVEYDH 185
           TL+   VP E+   + AA  L + +AER    D ++IGPD  A +     A+  G  +  
Sbjct: 136 TLQEA-VPLEDAVTLCAAPALARLIAERHP--DALLIGPDAEALQWIEAAAAEHGFAHGV 192

Query: 186 LEKKRLSGDEVEIHPKELDVEGRTVVLVDDMIDTGGTMVEAARALRDQGAGTLYAACTHA 245
             K R    +VEI   EL   GR VVL+DD+  +G T+ +AA  L   GA ++  A THA
Sbjct: 193 CSKVRHGDHQVEIALPELQFAGRHVVLLDDVASSGRTLAQAAEKLLAAGAASVDVAVTHA 252

Query: 246 LLTRNAATRLLASGFEDIIATDTVPNPFEKVSVAPPVAEAVENL 289
           L   +A   +  +G   + +TD + +    VS+AP +AEA+  L
Sbjct: 253 LFAGDALQVIRDAGVGHVWSTDCIAHGSNAVSMAPQLAEALRPL 296


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: 198
Number of extensions: 9
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
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 GFF3459 Psest_3524 (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.749.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    5.8e-54  169.0   0.0    7.3e-54  168.7   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3459  Psest_3524 ribose-phosphate pyro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3459  Psest_3524 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.7   0.0   7.3e-54   7.3e-54       9     296 ..      11     294 ..       4     297 .. 0.91

  Alignments for each domain:
  == domain 1  score: 168.7 bits;  conditional E-value: 7.3e-54
                           TIGR01251   9 skelaekvaknlglelgdvevkkFadgElyvrie....esvrgkdvfiivqstsapvndalmellllidalkras 79 
                                         +++ a ++a++ gl   ++e ++F+d+El  r+     e++   ++ +i        n++l+elll++  ++r +
  lcl|FitnessBrowser__psRCH2:GFF3459  11 ERAAALRLAEACGLTAAQIERHRFPDDELRLRLPladgEAI--AEQLVI-YRGLDHPNEKLVELLLIAGEARRLG 82 
                                         5667889999**********************963222344..356777.788889******************* PP

                           TIGR01251  80 aksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFd.vpven...lsaspkli 150
                                         ak++ +v Py++Y Rqd  ++++e +s +++++ll+    d ++tvd H + +    + vp+e+   l a+p l+
  lcl|FitnessBrowser__psRCH2:GFF3459  83 AKRLVLVTPYLAYMRQDIAFNPGEVVSQRVIGQLLAGQ-FDGLITVDPHLHRVATLQEaVPLEDavtLCAAPALA 156
                                         **************************************.************9999988888764333899***** PP

                           TIGR01251 151 eelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDDiisTggT 225
                                         + ++++   + +++ PD+ a+++ +++a++ g    +  K+R+  + +ve+   +++ +g++vv++DD+ s+g T
  lcl|FitnessBrowser__psRCH2:GFF3459 157 RLIAER-HPDALLIGPDAEALQWIEAAAAEHGFAHGVCSKVRHG-DHQVEIALPELQFAGRHVVLLDDVASSGRT 229
                                         ***997.889999******************************5.55**************************** PP

                           TIGR01251 226 lvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilveekklpkvseisvapliaeaia 296
                                         l++aae L  +GA +v va+th++f+gdAl+ ++ agv +v +t+ i++        + +s+ap +aea++
  lcl|FitnessBrowser__psRCH2:GFF3459 230 LAQAAEKLLAAGAASVDVAVTHALFAGDALQVIRDAGVGHVWSTDCIAH------GSNAVSMAPQLAEALR 294
                                         *************************************************......8889999999999985 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: 00:00:00.00
# Mc/sec: 10.94
//
[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