Alignments for a candidate for prs in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Dyella japonica UNC79MFTsu3.2

Align Ribose-phosphate pyrophosphokinase; RPPK; 5-phospho-D-ribosyl alpha-1-diphosphate synthase; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PRPP synthase; PRPPase; EC 2.7.6.1 (characterized)
to candidate N515DRAFT_3805 N515DRAFT_3805 ribose-phosphate pyrophosphokinase

Query= SwissProt::P0A1V6
         (315 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3805
          Length = 320

 Score =  383 bits (983), Expect = e-111
 Identities = 192/309 (62%), Positives = 248/309 (80%), Gaps = 1/309 (0%)

Query: 6   LFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPTND 65
           LF GNA   LA+ +A RL   LG A VGRFSDGE  ++I ENVR  ++F+IQ T AP+ +
Sbjct: 10  LFTGNAHRALAEDVATRLGVPLGKALVGRFSDGETQIEIEENVRRQEVFVIQPTGAPSAE 69

Query: 66  NLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVDRV 125
           NL EL+ +VDAL+RASA  +TAV+PYFGYARQDRR RSARVPITAK+VA  + +VGVDRV
Sbjct: 70  NLFELLTLVDALKRASAASVTAVMPYFGYARQDRRPRSARVPITAKMVAKMIGTVGVDRV 129

Query: 126 LTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQ-LNLDNPIVVSPDIGGVVRARAIAKLL 184
           LTVDLHA+QIQGFFD+PVDNV+ SP+LL D+ +  ++DN IVVSPD+GGVVRARA+AK L
Sbjct: 130 LTVDLHADQIQGFFDIPVDNVYASPLLLADIWRNHSMDNLIVVSPDVGGVVRARALAKRL 189

Query: 185 NDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAKRV 244
           +D D+AIIDKRRP+ANV+ VM+IIGDV G+ CVLVDD++DT GTLC AA ALKERGA++V
Sbjct: 190 DDADLAIIDKRRPKANVATVMNIIGDVDGKTCVLVDDIVDTAGTLCAAAAALKERGARKV 249

Query: 245 FAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGMLAEAIRRIS 304
            AY  HP+ SG A +N+ NS +D++VV +T+PL  E +A   +R L+++ +LAE IRRI+
Sbjct: 250 VAYCVHPVLSGAAISNIENSQLDQLVVTNTLPLRPEAQACAKIRQLSVAELLAETIRRIA 309

Query: 305 NEESISAMF 313
             ES+S+++
Sbjct: 310 FGESVSSLY 318


Lambda     K      H
   0.322    0.137    0.386 

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: 303
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: 315
Length of database: 320
Length adjustment: 27
Effective length of query: 288
Effective length of database: 293
Effective search space:    84384
Effective search space used:    84384
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate N515DRAFT_3805 N515DRAFT_3805 (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.30407.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.9e-119  383.1   0.2   4.5e-119  382.9   0.2    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3805  N515DRAFT_3805 ribose-phosphate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3805  N515DRAFT_3805 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.9   0.2  4.5e-119  4.5e-119       2     308 ..       9     318 ..       8     319 .. 0.98

  Alignments for each domain:
  == domain 1  score: 382.9 bits;  conditional E-value: 4.5e-119
                                    TIGR01251   2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalme 67 
                                                  +++ g+++++lae va +lg++lg++ v +F+dgE++++iee+vr ++vf+i q t ap  ++l+e
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3805   9 MLFTGNAHRALAEDVATRLGVPLGKALVGRFSDGETQIEIEENVRRQEVFVI-QPTGAPSAENLFE 73 
                                                  6899************************************************.99999******** PP

                                    TIGR01251  68 llllidalkrasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqi 132
                                                  ll+l+dalkrasa svtav+Py+gYaRqd++ +  r pi+ak+vak++ ++G+drvltvdlH++qi
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3805  74 LLTLVDALKRASAASVTAVMPYFGYARQDRRPRsARVPITAKMVAKMIGTVGVDRVLTVDLHADQI 139
                                                  ******************************97758******************************* PP

                                    TIGR01251 133 qgfFdvpvenlsaspklieelkkke.lknlvvvsPDkGaverakkvakklg.lelaiieKeRdske 196
                                                  qgfFd+pv+n++asp l++++ +++ ++nl+vvsPD G+v ra+++ak+l+ ++laii+K+R+ k+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3805 140 QGFFDIPVDNVYASPLLLADIWRNHsMDNLIVVSPDVGGVVRARALAKRLDdADLAIIDKRRP-KA 204
                                                  ********************999998*************************9***********.89 PP

                                    TIGR01251 197 nevevtnllgdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeag 262
                                                  n+++v+n++gdv+gk++v+vDDi++T+gTl++aa +Lke+GA+kv+++++h+v+sg A++++++++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3805 205 NVATVMNIIGDVDGKTCVLVDDIVDTAGTLCAAAAALKERGARKVVAYCVHPVLSGAAISNIENSQ 270
                                                  9***************************************************************** PP

                                    TIGR01251 263 veevivtntilv.ee.kklpkvseisvapliaeaiarihenesvsslf 308
                                                  +++++vtnt++   e +++ k++++sva+l+ae+i+ri+ +esvssl+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3805 271 LDQLVVTNTLPLrPEaQACAKIRQLSVAELLAETIRRIAFGESVSSLY 318
                                                  ************8556******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (320 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: 00:00:00.01
# Mc/sec: 6.71
//
[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