Alignments for a candidate for prs in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Pseudomonas putida KT2440

Align Ribose-phosphate pyrophosphokinase; RPPK; EC 2.7.6.1; 5-phospho-D-ribosyl alpha-1-diphosphate synthase; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PRPP synthase; PRPPase (uncharacterized)
to candidate PP_2744 PP_2744 Ribose-phosphate pyrophosphokinase family protein

Query= curated2:P75044
         (328 letters)



>FitnessBrowser__Putida:PP_2744
          Length = 319

 Score =  138 bits (347), Expect = 2e-37
 Identities = 97/322 (30%), Positives = 162/322 (50%), Gaps = 22/322 (6%)

Query: 7   VVFSLSKTHDLVSRICQKLKMPMGLITHNEFADGETYIRFEESVRNKDVFIFQSTCAPVN 66
           ++F+L  + D  + + Q+L   +      ++ DGE      ESV  + V +F S     +
Sbjct: 7   LLFALQGSQDYGNAVAQRLGRKLSAHEERDYEDGEHKCWPGESVDGRSVIVFHSLYGDAH 66

Query: 67  ----DSLMELLIAIDALKRGSAKSITAILPYYGYARQDRKTMGREPITSKLVADLLTTAG 122
               D L  LL    ALK  +A+ +TA+ PY  Y R+DRK   ++ I ++ VA L+ + G
Sbjct: 67  HSAHDKLCRLLFFCGALKDAAARQVTAVTPYLCYGRKDRKVEFQDAIITRHVARLMESCG 126

Query: 123 VSRVALTDIHSDQT-QGFFNIPVDTLRTYHVFLTRTVELLGKKDLVVVSPDYGGVKRARL 181
           V R+   D+H+       + IP   L+   +F  R   LLG++ + VVSPD GGVKRA  
Sbjct: 127 VDRIVALDVHNPSAFDNAYRIPSWNLQCTQLFAQRLAPLLGEQAVTVVSPDIGGVKRAEQ 186

Query: 182 IATSL------ELPLAIIDKRRPAHNVAESINVLGEVANKNCLIVDDMIDTGGTVIAAAK 235
              +L       + +A+++K R    ++   +++G VA    ++ DD+I TG T++ AA+
Sbjct: 187 FRQALAHLLARPVSVAMMEKHRQQAGLSGE-HLVGNVAGSTVIVFDDLISTGQTLLRAAQ 245

Query: 236 LLREHHAKKVCVMATHGLFNGEAPQRFQKAFNEGLVDYLFVSNSIPQTKFD-QC-PQFQV 293
             R+  A ++   ATHGLF         + F+ G  + + V++SI   +   +C  Q  +
Sbjct: 246 ACRQAGASRMLAAATHGLFTTGG-----ELFDSGAFERVLVADSIAPFRLPVRCLEQLDI 300

Query: 294 IDLAPLFEEVLLCYANNSSISA 315
           +D + L  E+L   AN S   A
Sbjct: 301 VDTSALVAELL---ANRSGPGA 319


Lambda     K      H
   0.323    0.137    0.398 

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: 244
Number of extensions: 15
Number of successful extensions: 4
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: 328
Length of database: 319
Length adjustment: 28
Effective length of query: 300
Effective length of database: 291
Effective search space:    87300
Effective search space used:    87300
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 PP_2744 PP_2744 (Ribose-phosphate pyrophosphokinase family protein)
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.2663.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    5.7e-63  198.6   0.0    7.3e-63  198.3   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_2744  PP_2744 Ribose-phosphate pyropho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_2744  PP_2744 Ribose-phosphate pyrophosphokinase family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.3   0.0   7.3e-63   7.3e-63       3     297 ..       8     313 ..       7     316 .. 0.91

  Alignments for each domain:
  == domain 1  score: 198.3 bits;  conditional E-value: 7.3e-63
                           TIGR01251   3 ilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiiv...qstsapvndalmellllida 74 
                                         +++++ s++  ++va++lg +l   e + + dgE +    esv+g+ v+++       +++  d+l  ll+ + a
  lcl|FitnessBrowser__Putida:PP_2744   8 LFALQGSQDYGNAVAQRLGRKLSAHEERDYEDGEHKCWPGESVDGRSVIVFHslyGDAHHSAHDKLCRLLFFCGA 82 
                                         578899999************************************87777766666678899************* PP

                           TIGR01251  75 lkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseq.iqgfFdvpvenlsaspk 148
                                         lk+a a++vtav Py+ Y+R+d+k++  ++i  + va+l+e+ G+dr++++d+H++    +++++p  nl+  + 
  lcl|FitnessBrowser__Putida:PP_2744  83 LKDAAARQVTAVTPYLCYGRKDRKVEFQDAIITRHVARLMESCGVDRIVALDVHNPSaFDNAYRIPSWNLQCTQL 157
                                         ******************************************************98626899************* PP

                           TIGR01251 149 lieelkkke.lknlvvvsPDkGaverakkvakklg......lelaiieKeRdskenevevtnllgdvegkdvviv 216
                                         ++++l+     + ++vvsPD G+v+ra++++++l       +++a++eK+R+ ++   + ++l+g+v+g +v+++
  lcl|FitnessBrowser__Putida:PP_2744 158 FAQRLAPLLgEQAVTVVSPDIGGVKRAEQFRQALAhllarpVSVAMMEKHRQ-QA-GLSGEHLVGNVAGSTVIVF 230
                                         ******999889999**************9998752211335789*******.44.7****************** PP

                           TIGR01251 217 DDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee..kklpkvseisva 288
                                         DD+isTg Tl++aa++ +++GA++ ++aathg+f+    e +++  +e+v+v+++i+  +   + l+++  ++ +
  lcl|FitnessBrowser__Putida:PP_2744 231 DDLISTGQTLLRAAQACRQAGASRMLAAATHGLFTTG-GELFDSGAFERVLVADSIAPfRLpvRCLEQLDIVDTS 304
                                         **********************************976.5899**************9855467888999999999 PP

                           TIGR01251 289 pliaeaiar 297
                                          l+ae +a+
  lcl|FitnessBrowser__Putida:PP_2744 305 ALVAELLAN 313
                                         999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (319 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: 7.79
//
[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