Alignments for a candidate for prs in Dehalococcoides mccartyi 195

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Dehalococcoides mccartyi 195

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_010936212.1 DET_RS02375 ribose-phosphate diphosphokinase

Query= SwissProt::P14193
         (317 letters)



>NCBI__GCF_000011905.1:WP_010936212.1
          Length = 324

 Score =  332 bits (850), Expect = 1e-95
 Identities = 166/308 (53%), Positives = 223/308 (72%), Gaps = 1/308 (0%)

Query: 10  LKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPV 69
           LKIF+ N+NP+LAK +AD + VQ+GKC V +FS+  + + I+ES+R  D Y+IQ T  PV
Sbjct: 11  LKIFTGNANPDLAKAVADYLKVQMGKCEVFQFSNENIFVRIQESVRKKDVYVIQPTCSPV 70

Query: 70  NEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETAGATR 129
           N+ IMELLIM+DALKRAS++ I  V+PYYGY R D+K + R PITA+L A+LL  AGA+R
Sbjct: 71  NQSIMELLIMMDALKRASSERITAVLPYYGYGRTDKKDQPRVPITARLIADLLTAAGASR 130

Query: 130 VIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLEDIVIVSPDHGGVTRARKLADRL 189
           ++ LDLHAPQIQGFFD+P+D L    +L  YF+ K LED+V+V+ D G   +AR  A +L
Sbjct: 131 ILTLDLHAPQIQGFFDMPVDELTAENLLANYFKKKKLEDLVVVATDVGISKKARDFAAKL 190

Query: 190 KAPIAIIDKRRPRPN-VAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEV 248
            AP+AII+KRR   N +   +NI+G++EGK A+  DD IDTAG++    N L+  G KEV
Sbjct: 191 DAPLAIIEKRRMGNNDITRTINIIGDVEGKNALTFDDEIDTAGSLVGNVNILINKGVKEV 250

Query: 249 YACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRVHE 308
           Y+C THPVLSGPA++RI  S IKELVVT+SI L   KKI++   LS+ PL+ EAI R+H 
Sbjct: 251 YSCATHPVLSGPAIQRIAASPIKELVVTDSIPLTPPKKIDKITVLSIAPLIGEAIYRIHT 310

Query: 309 QQSVSYLF 316
             S+  ++
Sbjct: 311 GNSIGEMY 318


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: 264
Number of extensions: 5
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_010936212.1 DET_RS02375 (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.29600.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-115  370.9   0.3   2.3e-115  370.7   0.3    1.0  1  lcl|NCBI__GCF_000011905.1:WP_010936212.1  DET_RS02375 ribose-phosphate dip


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000011905.1:WP_010936212.1  DET_RS02375 ribose-phosphate diphosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.7   0.3  2.3e-115  2.3e-115       2     309 .]      12     319 ..      11     319 .. 0.98

  Alignments for each domain:
  == domain 1  score: 370.7 bits;  conditional E-value: 2.3e-115
                                 TIGR01251   2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelll 70 
                                               ki+ g+++++la++va++l++++g++ev +F+++++ vri+esvr kdv++i q t+ pvn+++mell+
  lcl|NCBI__GCF_000011905.1:WP_010936212.1  12 KIFTGNANPDLAKAVADYLKVQMGKCEVFQFSNENIFVRIQESVRKKDVYVI-QPTCSPVNQSIMELLI 79 
                                               89**************************************************.9*************** PP

                                 TIGR01251  71 lidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvp 139
                                               ++dalkras +++tav+PyygY+R dkk+++r pi+a+l+a+ll++aGa+r+lt+dlH++qiqgfFd+p
  lcl|NCBI__GCF_000011905.1:WP_010936212.1  80 MMDALKRASSERITAVLPYYGYGRTDKKDQPRVPITARLIADLLTAAGASRILTLDLHAPQIQGFFDMP 148
                                               ********************************************************************* PP

                                 TIGR01251 140 venlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdv 208
                                               v++l+a++ l++++kkk+l++lvvv+ D G  + a+++a+kl+++laiieK+R  ++   +++n++gdv
  lcl|NCBI__GCF_000011905.1:WP_010936212.1 149 VDELTAENLLANYFKKKKLEDLVVVATDVGISKKARDFAAKLDAPLAIIEKRRMGNNDITRTINIIGDV 217
                                               ******************************************************666666799****** PP

                                 TIGR01251 209 egkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilvee. 276
                                               egk+++ +DD i+T+g+lv  +++L +kG k+v+ +ath+v+sg+A++r+a + ++e++vt++i+ +  
  lcl|NCBI__GCF_000011905.1:WP_010936212.1 218 EGKNALTFDDEIDTAGSLVGNVNILINKGVKEVYSCATHPVLSGPAIQRIAASPIKELVVTDSIPLTPp 286
                                               ******************************************************************666 PP

                                 TIGR01251 277 kklpkvseisvapliaeaiarihenesvsslfd 309
                                               kk++k++++s+apli eai rih+++s+ +++d
  lcl|NCBI__GCF_000011905.1:WP_010936212.1 287 KKIDKITVLSIAPLIGEAIYRIHTGNSIGEMYD 319
                                               ****************************99986 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.87
//
[ok]

This GapMind analysis is from Apr 10 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