Alignments for a candidate for prs in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Dechlorosoma suillum PS

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 Dsui_1036 Dsui_1036 ribose-phosphate pyrophosphokinase

Query= SwissProt::P0A1V6
         (315 letters)



>FitnessBrowser__PS:Dsui_1036
          Length = 317

 Score =  403 bits (1036), Expect = e-117
 Identities = 203/311 (65%), Positives = 257/311 (82%), Gaps = 2/311 (0%)

Query: 4   MKLFAGNATPELAQRIANRL-YTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAP 62
           + +F GNA P+LA  + +RL    LG A+VGRFSDGEVSV+I E+VRG D+FI+QSTCAP
Sbjct: 6   LMVFTGNANPKLAADVVSRLGRRPLGRASVGRFSDGEVSVEIEEHVRGHDVFILQSTCAP 65

Query: 63  TNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGV 122
           +ND LMEL+VMVDAL+RASAGRITA IPYFGYARQDRR RS+RVPI AK+VAD L++ GV
Sbjct: 66  SNDTLMELLVMVDALKRASAGRITAAIPYFGYARQDRRSRSSRVPIAAKLVADLLTAAGV 125

Query: 123 DRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAK 182
           DRVLT+DLHAEQIQGFFD+PVDNV+  PILLED+ + N +N +VVSPD GGVVRAR++AK
Sbjct: 126 DRVLTMDLHAEQIQGFFDIPVDNVYALPILLEDIQKQNHENLLVVSPDHGGVVRARSLAK 185

Query: 183 LLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAK 242
            L + D+AIIDKRRP+ANVS+VM+IIG+V GR C+++DD++DT GTLCKAA ALK  GA+
Sbjct: 186 RL-ECDLAIIDKRRPKANVSEVMNIIGEVDGRTCIIMDDIVDTAGTLCKAASALKANGAQ 244

Query: 243 RVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGMLAEAIRR 302
           +V AY THP+ SG A   + +S +DE+VV DTIPL D+  A   +R L+++ +LAE IRR
Sbjct: 245 KVVAYCTHPVLSGAAVERVNSSDLDELVVTDTIPLRDDAMACSRIRQLSVAELLAETIRR 304

Query: 303 ISNEESISAMF 313
           ISNE+S+S++F
Sbjct: 305 ISNEDSVSSLF 315


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: 290
Number of extensions: 8
Number of successful extensions: 3
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: 317
Length adjustment: 27
Effective length of query: 288
Effective length of database: 290
Effective search space:    83520
Effective search space used:    83520
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 Dsui_1036 Dsui_1036 (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.15532.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.4e-126  407.6   0.4   1.5e-126  407.4   0.4    1.0  1  lcl|FitnessBrowser__PS:Dsui_1036  Dsui_1036 ribose-phosphate pyrop


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_1036  Dsui_1036 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.4   0.4  1.5e-126  1.5e-126       2     308 ..       7     315 ..       6     316 .. 0.98

  Alignments for each domain:
  == domain 1  score: 407.4 bits;  conditional E-value: 1.5e-126
                         TIGR01251   2 kilsgssskelaekvaknlg.lelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidalkr 77 
                                       +++ g+++++la+ v  +lg  +lg+++v +F+dgE++v+iee+vrg+dvfi+ qst+ap nd lmell+++dalkr
  lcl|FitnessBrowser__PS:Dsui_1036   7 MVFTGNANPKLAADVVSRLGrRPLGRASVGRFSDGEVSVEIEEHVRGHDVFIL-QSTCAPSNDTLMELLVMVDALKR 82 
                                       89***********99999972579*****************************.*********************** PP

                         TIGR01251  78 asaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspklieel 153
                                       asa+++ta iPy+gYaRqd++ + sr pi+aklva+ll++aG+drvlt+dlH+eqiqgfFd+pv+n++a p l+e++
  lcl|FitnessBrowser__PS:Dsui_1036  83 ASAGRITAAIPYFGYARQDRRSRsSRVPIAAKLVADLLTAAGVDRVLTMDLHAEQIQGFFDIPVDNVYALPILLEDI 159
                                       ********************98768**************************************************** PP

                         TIGR01251 154 kkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDDiisTggTlvkaa 230
                                       +k++ +nl+vvsPD+G+v ra+++ak+l+++laii+K+R+ k+n+ ev+n++g+v+g++++i+DDi++T+gTl+kaa
  lcl|FitnessBrowser__PS:Dsui_1036 160 QKQNHENLLVVSPDHGGVVRARSLAKRLECDLAIIDKRRP-KANVSEVMNIIGEVDGRTCIIMDDIVDTAGTLCKAA 235
                                       ****************************************.899********************************* PP

                         TIGR01251 231 elLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kklpkvseisvapliaeaiarihenesvs 305
                                       ++Lk +GA+kv++++th+v+sg A+er++++ ++e++vt+ti+  ++  ++++++++sva+l+ae+i+ri+++ svs
  lcl|FitnessBrowser__PS:Dsui_1036 236 SALKANGAQKVVAYCTHPVLSGAAVERVNSSDLDELVVTDTIPLrDDaMACSRIRQLSVAELLAETIRRISNEDSVS 312
                                       ********************************************877899*************************** PP

                         TIGR01251 306 slf 308
                                       slf
  lcl|FitnessBrowser__PS:Dsui_1036 313 SLF 315
                                       **9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (317 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: 10.73
//
[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