Alignments for a candidate for prs in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Acidovorax sp. GW101-3H11

Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate Ac3H11_3452 Ribose-phosphate pyrophosphokinase (EC 2.7.6.1)

Query= BRENDA::P0A719
         (315 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3452
          Length = 324

 Score =  409 bits (1050), Expect = e-119
 Identities = 204/313 (65%), Positives = 256/313 (81%), Gaps = 2/313 (0%)

Query: 2   PDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCA 61
           PD  +F GNA P +A  IA  L T+LG A VGRFSDGEV+V+I +NVR  D+F++QSTCA
Sbjct: 6   PDFMVFTGNANPGMAAEIAQHLGTTLGAADVGRFSDGEVTVEIKQNVRARDVFVVQSTCA 65

Query: 62  PTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVG 121
           PTN+NLMEL++MVDAL+RASA RI+AVIPYFGYARQDRR RS RVPITAKVVA+ L +VG
Sbjct: 66  PTNENLMELLIMVDALKRASAERISAVIPYFGYARQDRRPRSTRVPITAKVVANMLQAVG 125

Query: 122 VDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIA 181
           V RVLT+DLHA+QIQGFFD+PVDN++ SP+LL D+ Q N ++ IVVSPD+GGVVRARA+A
Sbjct: 126 VARVLTMDLHADQIQGFFDIPVDNIYASPVLLGDLRQKNYEDLIVVSPDVGGVVRARALA 185

Query: 182 KLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGA 241
           K L   D+AIIDKRRP+ANVS+VMH+IG++ GR+CV++DDMIDT GTL KAAE LKERGA
Sbjct: 186 KQLG-CDLAIIDKRRPKANVSEVMHVIGEIEGRNCVIMDDMIDTAGTLVKAAEVLKERGA 244

Query: 242 KRVFAYATHPIFSGNAANNL-RNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAI 300
           K V+AY THPIFSG A   + + S +DEVVV +TIPLSD  K    +R L+++ ++AE I
Sbjct: 245 KSVYAYCTHPIFSGPAIERIAKGSALDEVVVTNTIPLSDNAKGCTKIRQLSVAPLIAETI 304

Query: 301 RRISNEESISAMF 313
           +RI+  ES+ ++F
Sbjct: 305 QRIAKGESVMSLF 317


Lambda     K      H
   0.321    0.137    0.385 

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: 323
Number of extensions: 5
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: 324
Length adjustment: 28
Effective length of query: 287
Effective length of database: 296
Effective search space:    84952
Effective search space used:    84952
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 Ac3H11_3452 (Ribose-phosphate pyrophosphokinase (EC 2.7.6.1))
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.18326.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   2.3e-129  416.7   0.7   2.6e-129  416.5   0.7    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3452  Ribose-phosphate pyrophosphokina


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3452  Ribose-phosphate pyrophosphokinase (EC 2.7.6.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.5   0.7  2.6e-129  2.6e-129       2     309 .]       9     318 ..       8     318 .. 0.98

  Alignments for each domain:
  == domain 1  score: 416.5 bits;  conditional E-value: 2.6e-129
                                        TIGR01251   2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvnd 63 
                                                      +++ g++++ +a+++a++lg+ lg ++v +F+dgE+ v+i+++vr +dvf++ qst+ap+n+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3452   9 MVFTGNANPGMAAEIAQHLGTTLGAADVGRFSDGEVTVEIKQNVRARDVFVV-QSTCAPTNE 69 
                                                      799*************************************************.********* PP

                                        TIGR01251  64 almellllidalkrasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvlt 124
                                                      +lmell+++dalkrasa++++aviPy+gYaRqd++ +  r pi+ak+va++l+++G+ rvlt
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3452  70 NLMELLIMVDALKRASAERISAVIPYFGYARQDRRPRsTRVPITAKVVANMLQAVGVARVLT 131
                                                      **********************************98758*********************** PP

                                        TIGR01251 125 vdlHseqiqgfFdvpvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklglela 186
                                                      +dlH++qiqgfFd+pv+n++asp+l+ +l++k+ ++l+vvsPD G+v ra+++ak+lg++la
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3452 132 MDLHADQIQGFFDIPVDNIYASPVLLGDLRQKNYEDLIVVSPDVGGVVRARALAKQLGCDLA 193
                                                      ************************************************************** PP

                                        TIGR01251 187 iieKeRdskenevevtnllgdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathg 248
                                                      ii+K+R+ k+n+ ev++++g++eg+++vi+DD+i+T+gTlvkaae+Lke+GAk+v++++th+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3452 194 IIDKRRP-KANVSEVMHVIGEIEGRNCVIMDDMIDTAGTLVKAAEVLKERGAKSVYAYCTHP 254
                                                      *******.899*************************************************** PP

                                        TIGR01251 249 vfsgdAlerlaeag.veevivtntilv.ee.kklpkvseisvapliaeaiarihenesvssl 307
                                                      +fsg+A+er+a+   ++ev+vtnti+  ++ k + k++++svapliae+i ri+++esv sl
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3452 255 IFSGPAIERIAKGSaLDEVVVTNTIPLsDNaKGCTKIRQLSVAPLIAETIQRIAKGESVMSL 316
                                                      ***********98779***********766899***************************** PP

                                        TIGR01251 308 fd 309
                                                      f+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3452 317 FS 318
                                                      95 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.86
//
[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