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 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 Ac3H11_2203 Ribose-phosphate pyrophosphokinase (EC 2.7.6.1)

Query= curated2:Q8TUT6
         (291 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2203
          Length = 303

 Score =  142 bits (357), Expect = 1e-38
 Identities = 96/284 (33%), Positives = 150/284 (52%), Gaps = 11/284 (3%)

Query: 14  RRLAEELDAELAPVEEDRFPDGEQIVRVPPELDGTV----VVVHSMSPPQDENLVKAIIT 69
           +RLA+        +E  RFPDGE  +R+P +  G +    V++ S+  P +E LV+ ++ 
Sbjct: 20  QRLAQAAGLTAQAIERHRFPDGELKLRLPVDASGRLPQRAVLLRSLHQP-NEKLVELLLA 78

Query: 70  LDAARENGAEEVIAIVPYMAYSRQDRRFEPGEPVSFRAVARAVSANADALITVD--LHEP 127
              AR+ GA+ +  + PY+AY RQD  F PGE VS + V   ++   DA+ITVD  LH  
Sbjct: 79  ARTARQLGAQHLTLVAPYLAYMRQDIAFHPGEAVSQQVVGGFLAGLFDAVITVDPHLHRI 138

Query: 128 GTLKYFDVPAENV--SAAEELGKYLAERFEGEDLVVIGPDEGARELAREVASICGVEYDH 185
             L+      + V  S AE L   +A+R  G   +++GPD  + +   + A+    ++  
Sbjct: 139 ERLEQAMPVTQAVVLSGAEPLADLIAQRRPGA--LLVGPDGESAQWIAQAAARHSFDHAV 196

Query: 186 LEKKRLSGDEVEIHPKELDVEGRTVVLVDDMIDTGGTMVEAARALRDQGAGTLYAACTHA 245
             K R     V I    L+ +GR VVL+DDM  TG T+  A R L   GA ++  A THA
Sbjct: 197 CTKVRHGDRNVAIELPALNAQGRAVVLLDDMASTGRTLALATRLLLQAGAASVDVAVTHA 256

Query: 246 LLTRNAATRLLASGFEDIIATDTVPNPFEKVSVAPPVAEAVENL 289
           L   +A   L  +G  ++ +TD +P+P   V++A P+A A+  +
Sbjct: 257 LFAGDALQVLTEAGVGEVWSTDCIPHPSNAVAMAGPLAAALHRV 300


Lambda     K      H
   0.314    0.134    0.370 

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: 188
Number of extensions: 10
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: 291
Length of database: 303
Length adjustment: 26
Effective length of query: 265
Effective length of database: 277
Effective search space:    73405
Effective search space used:    73405
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate Ac3H11_2203 (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.9800.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
    2.8e-56  176.7   0.0    3.4e-56  176.4   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2203  Ribose-phosphate pyrophosphokina


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2203  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 !  176.4   0.0   3.4e-56   3.4e-56      12     283 ..      18     285 ..       9     302 .. 0.90

  Alignments for each domain:
  == domain 1  score: 176.4 bits;  conditional E-value: 3.4e-56
                                        TIGR01251  12 laekvaknlglelgdvevkkFadgElyvri..eesvrgkdvfiivqstsapvndalmellll 71 
                                                       a+++a+++gl    +e ++F+dgEl+ r+  + s r  +++++  s + + n++l+elll+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2203  18 PAQRLAQAAGLTAQAIERHRFPDGELKLRLpvDASGRLPQRAVLLRSLH-QPNEKLVELLLA 78 
                                                      58999**********************9971155566669999988888.69********** PP

                                        TIGR01251  72 idalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiq 133
                                                      + ++++ +a+++t+v+Py++Y Rqd  ++++e++s ++v+ +l+ +  d v+tvd H + i+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2203  79 ARTARQLGAQHLTLVAPYLAYMRQDIAFHPGEAVSQQVVGGFLAGL-FDAVITVDPHLHRIE 139
                                                      **********************************************.*************99 PP

                                        TIGR01251 134 gfFd.vpven...lsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKe 191
                                                         + +pv++   ls+++ l++ ++++     ++v PD  ++++  ++a++   + a+  K+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2203 140 RLEQaMPVTQavvLSGAEPLADLIAQR-RPGALLVGPDGESAQWIAQAAARHSFDHAVCTKV 200
                                                      887766665433389999999999986.788899**************************** PP

                                        TIGR01251 192 RdskenevevtnllgdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgd 253
                                                      R+  + +v ++   ++ +g+ vv++DD+ sTg Tl+ a +lL ++GA +v va+th++f+gd
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2203 201 RH-GDRNVAIELPALNAQGRAVVLLDDMASTGRTLALATRLLLQAGAASVDVAVTHALFAGD 261
                                                      **.566******************************************************** PP

                                        TIGR01251 254 Alerlaeagveevivtntilveekklpkvs 283
                                                      Al+ l+eagv ev +t+ i++        +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2203 262 ALQVLTEAGVGEVWSTDCIPH------PSN 285
                                                      ********************9......333 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (303 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.02
//
[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