Alignments for a candidate for prs in Methylocapsa aurea KYG T

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Methylocapsa aurea KYG T

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 WP_036263710.1 DL86_RS16755 ribose-phosphate pyrophosphokinase

Query= curated2:Q83YI7
         (318 letters)



>NCBI__GCF_000746085.1:WP_036263710.1
          Length = 323

 Score =  179 bits (454), Expect = 8e-50
 Identities = 117/327 (35%), Positives = 179/327 (54%), Gaps = 23/327 (7%)

Query: 10  LKIFSLNSNRELAEEIAKEVGIELGKSSVTHFSDGEIQINIEESIRGCHVYVIQST---- 65
           +++F+LN++R  AE+IA  +G+EL       F DGE +     S+RG  VYV+QS     
Sbjct: 1   MQLFTLNASRTFAEKIAAALGVELSSHEEREFEDGEHKARPLASVRGEDVYVVQSLHGGP 60

Query: 66  SNPVNQNLMELLIMIDALKRASAATINIVMPYYGYARQDRKARSREPITAKLVANLIETA 125
               N  L  LL  +  +K   AA +  V+PY  YAR+DR+ + R+P+T + VA L+E A
Sbjct: 61  DQSPNDKLCRLLFFLATMKENGAARVTAVIPYLAYARKDRQTKPRDPVTTRYVAELLEAA 120

Query: 126 GATRMITLDMH-APQIQGFFDIPIDHLNAVRLLSNYFGERHLG----DDLVVVSPDHGGV 180
           GA  ++TLD+H     Q  F     HL+  RL    F ER +        VV SPD GGV
Sbjct: 121 GADCVVTLDVHNIVAFQNAFRCETIHLDTRRL----FAERAVALIGEAAAVVASPDPGGV 176

Query: 181 TRARKMADRLKAPI------AIIDKRRPRPNVAEVMNIVGNVEGKVCIIIDDIIDTAGTI 234
            RA+   + L+  +      A ++KRR    V+  + +VG+V G   +I+DD+I   GT+
Sbjct: 177 KRAQLFREMLETMLGRPVGSAFMEKRRSAGVVSGNL-LVGDVAGATVLIVDDLISGGGTM 235

Query: 235 TLAAKALREAGATKVYACCSHPVLSGPAMKRIEESPIEKLVVTNSIA--LPEDKWI-DKM 291
             A+ A RE GA  +YA  +H + +G A   +  S + K  VT+++     +DK +  ++
Sbjct: 236 ARASHACREGGAKTIYAFAAHGLFTGEAASALRHSDLAKTFVTDTVPPFRLDDKLVGGRV 295

Query: 292 EQLSVAPLLGEAIVRVHENASVSSLFE 318
           E LS APL  +AI  +HE+ S+++L E
Sbjct: 296 EILSAAPLFAKAIRALHEDGSINALLE 322


Lambda     K      H
   0.319    0.135    0.378 

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: 198
Number of extensions: 12
Number of successful extensions: 5
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: 318
Length of database: 323
Length adjustment: 28
Effective length of query: 290
Effective length of database: 295
Effective search space:    85550
Effective search space used:    85550
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_036263710.1 DL86_RS16755 (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.19431.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    4.7e-80  254.7   0.0    5.3e-80  254.6   0.0    1.0  1  lcl|NCBI__GCF_000746085.1:WP_036263710.1  DL86_RS16755 ribose-phosphate py


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000746085.1:WP_036263710.1  DL86_RS16755 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.6   0.0   5.3e-80   5.3e-80       1     308 [.       1     321 [.       1     322 [. 0.92

  Alignments for each domain:
  == domain 1  score: 254.6 bits;  conditional E-value: 5.3e-80
                                 TIGR01251   1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqsts....apvndal 65 
                                               ++++ +++s+++aek+a +lg+el + e ++F dgE + r   svrg+dv+++ qs +    ++ nd+l
  lcl|NCBI__GCF_000746085.1:WP_036263710.1   1 MQLFTLNASRTFAEKIAAALGVELSSHEEREFEDGEHKARPLASVRGEDVYVV-QSLHggpdQSPNDKL 68 
                                               67899************************************************.55542333578**** PP

                                 TIGR01251  66 mellllidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHs.eqiq 133
                                                 ll+ + ++k+++a +vtaviPy++YaR+d+++k+r+p++ + va+lle+aGad v+t+d+H+  + q
  lcl|NCBI__GCF_000746085.1:WP_036263710.1  69 CRLLFFLATMKENGAARVTAVIPYLAYARKDRQTKPRDPVTTRYVAELLEAAGADCVVTLDVHNiVAFQ 137
                                               ***************************************************************94578* PP

                                 TIGR01251 134 gfFdvpvenlsaspklieelkkke.lknlvvvsPDkGaverakkvakklglel......aiieKeRdsk 195
                                               ++F+ +  +l++ + ++e+  + +     vv sPD G+v+ra+ +++ l++ l      a++eK+R  +
  lcl|NCBI__GCF_000746085.1:WP_036263710.1 138 NAFRCETIHLDTRRLFAERAVALIgEAAAVVASPDPGGVKRAQLFREMLETMLgrpvgsAFMEKRRS-A 205
                                               **********************99899999***************9998865433334499*****9.5 PP

                                 TIGR01251 196 enevevtnllgdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagve 264
                                                 +v+ + l+gdv+g +v+ivDD+is ggT+++a+++ +e GAk +++ a hg+f+g+A++ l+++ + 
  lcl|NCBI__GCF_000746085.1:WP_036263710.1 206 G-VVSGNLLVGDVAGATVLIVDDLISGGGTMARASHACREGGAKTIYAFAAHGLFTGEAASALRHSDLA 273
                                               5.9****************************************************************** PP

                                 TIGR01251 265 evivtntilv...ee.kklpkvseisvapliaeaiarihenesvsslf 308
                                               + +vt+t++    ++     +v+ +s apl+a+ai++ he+ s+++l+
  lcl|NCBI__GCF_000746085.1:WP_036263710.1 274 KTFVTDTVPPfrlDDkLVGGRVEILSAAPLFAKAIRALHEDGSINALL 321
                                               ********9753333345689************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (323 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: 8.34
//
[ok]

This GapMind analysis is from Apr 10 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