Alignments for a candidate for prs in Salinicoccus carnicancri Crm

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Salinicoccus carnicancri Crm

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_017550051.1 C792_RS14930 ribose-phosphate diphosphokinase

Query= SwissProt::P14193
         (317 letters)



>NCBI__GCF_000330705.1:WP_017550051.1
          Length = 324

 Score =  474 bits (1220), Expect = e-138
 Identities = 233/318 (73%), Positives = 278/318 (87%), Gaps = 3/318 (0%)

Query: 2   SNQYGDKNLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYI 61
           SNQY + +L++FSL  N  LA+EIA+ +G+ LGK +V  FSD EVQ+NIEES+RGCD ++
Sbjct: 5   SNQYKNSSLRLFSLKGNEPLAEEIAEQIGIPLGKITVQHFSDEEVQVNIEESVRGCDVFV 64

Query: 62  IQSTSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANL 121
           +Q TS PVNEH+M+LLIM+DALKRASA TINIV+PYYGYARQDRK+R+REPITAKL ANL
Sbjct: 65  VQPTSQPVNEHLMQLLIMIDALKRASAATINIVMPYYGYARQDRKSRAREPITAKLVANL 124

Query: 122 LETAGATRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYF---EGKNLEDIVIVSPDHGG 178
           +ETAGA RVI+LDLHAPQIQGFFDIPIDHLMGVPIL +YF   +  N +++V+VSPDHGG
Sbjct: 125 IETAGADRVISLDLHAPQIQGFFDIPIDHLMGVPILSDYFLEHKDLNFDEVVVVSPDHGG 184

Query: 179 VTRARKLADRLKAPIAIIDKRRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAAN 238
           VTRARK+ADRLK PIAIIDKRRP+PNVAEVMNIVG IEG+TAI+IDDIIDT GT+ LAA 
Sbjct: 185 VTRARKMADRLKTPIAIIDKRRPKPNVAEVMNIVGEIEGRTAIIIDDIIDTGGTMKLAAQ 244

Query: 239 ALVENGAKEVYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPL 298
           AL++ GAKEVYACCTHPVLSGPA+ RI  S IKELVVTNSI+LPEEKKI++   LSVG L
Sbjct: 245 ALLDKGAKEVYACCTHPVLSGPAISRIEESVIKELVVTNSIQLPEEKKIDKIVGLSVGEL 304

Query: 299 LAEAIIRVHEQQSVSYLF 316
           +A+AI+RV+E++SVS LF
Sbjct: 305 MAQAIVRVYEEESVSILF 322


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: 332
Number of extensions: 9
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: 324
Length adjustment: 28
Effective length of query: 289
Effective length of database: 296
Effective search space:    85544
Effective search space used:    85544
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_017550051.1 C792_RS14930 (ribose-phosphate diphosphokinase)
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.2801530.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.2e-128  412.5   0.6   4.8e-128  412.4   0.6    1.0  1  NCBI__GCF_000330705.1:WP_017550051.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330705.1:WP_017550051.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.4   0.6  4.8e-128  4.8e-128       2     309 .]      14     323 ..      13     323 .. 0.99

  Alignments for each domain:
  == domain 1  score: 412.4 bits;  conditional E-value: 4.8e-128
                             TIGR01251   2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllida 74 
                                           +++s++ ++ lae++a++ g++lg+++v++F+d+E++v+ieesvrg+dvf++ q ts+pvn++lm+ll++ida
  NCBI__GCF_000330705.1:WP_017550051.1  14 RLFSLKGNEPLAEEIAEQIGIPLGKITVQHFSDEEVQVNIEESVRGCDVFVV-QPTSQPVNEHLMQLLIMIDA 85 
                                           68999***********************************************.******************** PP

                             TIGR01251  75 lkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsasp 147
                                           lkrasa ++++v+PyygYaRqd+k + repi+aklva+l+e+aGadrv+ +dlH++qiqgfFd+p+++l++ p
  NCBI__GCF_000330705.1:WP_017550051.1  86 LKRASAATINIVMPYYGYARQDRKSRAREPITAKLVANLIETAGADRVISLDLHAPQIQGFFDIPIDHLMGVP 158
                                           ************************************************************************* PP

                             TIGR01251 148 klieelkkke...lknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivD 217
                                            l +++ +++    +++vvvsPD+G+v+ra+k+a++l++++aii+K+R+ k n++ev+n++g++eg++++i+D
  NCBI__GCF_000330705.1:WP_017550051.1 159 ILSDYFLEHKdlnFDEVVVVSPDHGGVTRARKMADRLKTPIAIIDKRRP-KPNVAEVMNIVGEIEGRTAIIID 230
                                           ******998888899**********************************.999******************** PP

                             TIGR01251 218 DiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.eekklpkvseisvap 289
                                           Dii+TggT+  aa++L +kGAk+v++++th+v+sg+A++r++e++++e++vtn+i+  eekk++k+  +sv +
  NCBI__GCF_000330705.1:WP_017550051.1 231 DIIDTGGTMKLAAQALLDKGAKEVYACCTHPVLSGPAISRIEESVIKELVVTNSIQLpEEKKIDKIVGLSVGE 303
                                           *********************************************************999************* PP

                             TIGR01251 290 liaeaiarihenesvsslfd 309
                                           l+a+ai+r++e+esvs lfd
  NCBI__GCF_000330705.1:WP_017550051.1 304 LMAQAIVRVYEEESVSILFD 323
                                           ******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (324 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: 13.10
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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