Alignments for a candidate for prs in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

Align Ribose-phosphate pyrophosphokinase; RPPK; 5-phospho-D-ribosyl alpha-1-diphosphate synthase; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PPRibP synthase; PRPP synthase; PRPPase; EC 2.7.6.1 (characterized)
to candidate WP_012408935.1 NPUN_RS11925 ribose-phosphate pyrophosphokinase

Query= SwissProt::P14193
         (317 letters)



>NCBI__GCF_000020025.1:WP_012408935.1
          Length = 338

 Score =  348 bits (892), Expect = e-100
 Identities = 173/308 (56%), Positives = 227/308 (73%), Gaps = 1/308 (0%)

Query: 10  LKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPV 69
           L++FS ++N +L++E+A  VG+ LG     RF+DGE+ + I+ESIRGCD Y+IQ    PV
Sbjct: 30  LRLFSGSANLQLSQEVARYVGMDLGPMIRKRFADGELYVQIQESIRGCDVYLIQPCCQPV 89

Query: 70  NEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETAGATR 129
           N+H+MELLIMVDA +RASA+ +  VIPYYGYAR DRK   RE ITAKL ANL+  AGA R
Sbjct: 90  NDHLMELLIMVDACRRASARQVTAVIPYYGYARADRKTAGRESITAKLVANLITEAGANR 149

Query: 130 VIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLEDIVIVSPDHGGVTRARKLADRL 189
           V+A+DLH+ QIQG+FDIP DH+ G P+L +Y   K L D+V+VSPD GGV RAR  A +L
Sbjct: 150 VLAMDLHSAQIQGYFDIPFDHVYGSPVLLDYLASKELPDLVVVSPDVGGVARARAFAKKL 209

Query: 190 K-APIAIIDKRRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEV 248
             AP+AIIDKRR   NVAEV+NI+G+++GKTA+L+DD+IDT GTI   A  L E GA++V
Sbjct: 210 NDAPLAIIDKRRQAHNVAEVLNIIGDVKGKTAVLVDDMIDTGGTIAEGARLLREEGARQV 269

Query: 249 YACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRVHE 308
           YAC TH V S PA+ER+++   +E++VTN+I +PE  +  +   LSV  LL E I R+HE
Sbjct: 270 YACATHAVFSPPAMERLSSGLFEEVIVTNTIPIPENNRFPQLVVLSVANLLGETIWRIHE 329

Query: 309 QQSVSYLF 316
             SVS +F
Sbjct: 330 DTSVSSMF 337


Lambda     K      H
   0.319    0.137    0.383 

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: 270
Number of extensions: 11
Number of successful extensions: 2
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: 317
Length of database: 338
Length adjustment: 28
Effective length of query: 289
Effective length of database: 310
Effective search space:    89590
Effective search space used:    89590
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_012408935.1 NPUN_RS11925 (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.1282322.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-132  427.0   0.0   1.9e-132  426.8   0.0    1.0  1  NCBI__GCF_000020025.1:WP_012408935.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020025.1:WP_012408935.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.8   0.0  1.9e-132  1.9e-132       2     309 .]      31     338 .]      30     338 .] 0.99

  Alignments for each domain:
  == domain 1  score: 426.8 bits;  conditional E-value: 1.9e-132
                             TIGR01251   2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllida 74 
                                           +++sgs++ +l+++va+++g++lg++  k+FadgElyv+i+es+rg+dv++i q +++pvnd+lmell+++da
  NCBI__GCF_000020025.1:WP_012408935.1  31 RLFSGSANLQLSQEVARYVGMDLGPMIRKRFADGELYVQIQESIRGCDVYLI-QPCCQPVNDHLMELLIMVDA 102
                                           689*************************************************.******************** PP

                             TIGR01251  75 lkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsasp 147
                                           ++rasa++vtaviPyygYaR d+k+ +re+i+aklva+l++eaGa+rvl++dlHs qiqg+Fd+p++++++sp
  NCBI__GCF_000020025.1:WP_012408935.1 103 CRRASARQVTAVIPYYGYARADRKTAGRESITAKLVANLITEAGANRVLAMDLHSAQIQGYFDIPFDHVYGSP 175
                                           ************************************************************************* PP

                             TIGR01251 148 klieelkkkelknlvvvsPDkGaverakkvakklg.lelaiieKeRdskenevevtnllgdvegkdvvivDDi 219
                                           +l+++l++kel +lvvvsPD G+v+ra+++akkl+ ++laii+K+R+ ++n++ev n++gdv+gk++v+vDD+
  NCBI__GCF_000020025.1:WP_012408935.1 176 VLLDYLASKELPDLVVVSPDVGGVARARAFAKKLNdAPLAIIDKRRQ-AHNVAEVLNIIGDVKGKTAVLVDDM 247
                                           ***********************************9***********.999********************** PP

                             TIGR01251 220 isTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.eekklpkvseisvapli 291
                                           i+TggT++++a+lL+e+GA++v+++ath+vfs +A+erl++  +eevivtnti++ e++++p++ ++sva+l+
  NCBI__GCF_000020025.1:WP_012408935.1 248 IDTGGTIAEGARLLREEGARQVYACATHAVFSPPAMERLSSGLFEEVIVTNTIPIpENNRFPQLVVLSVANLL 320
                                           *******************************************************888*************** PP

                             TIGR01251 292 aeaiarihenesvsslfd 309
                                            e+i+rihe++svss+f+
  NCBI__GCF_000020025.1:WP_012408935.1 321 GETIWRIHEDTSVSSMFR 338
                                           ****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (338 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 12.73
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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