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.1162001.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 20.65
//
[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:

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:

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:

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:

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