GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prs in Sphingomonas indica Dd16

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 WP_085217580.1 B9N75_RS03680 ribose-phosphate pyrophosphokinase

Query= SwissProt::P0A1V6
         (315 letters)



>NCBI__GCF_900177405.1:WP_085217580.1
          Length = 311

 Score =  332 bits (850), Expect = 9e-96
 Identities = 172/312 (55%), Positives = 230/312 (73%), Gaps = 2/312 (0%)

Query: 4   MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63
           MKL +GN+   L + IA  L   + DA+V RF+D EV V+I+ENVRG D+F+IQST  P 
Sbjct: 1   MKLLSGNSNRPLVEAIAAYLEMPITDASVRRFADEEVFVEIHENVRGEDVFVIQSTAFPA 60

Query: 64  NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123
           NDNLMEL++ +DAL+RASA RITAV+PYFGYARQDR+    R PI+AK+VA+ ++  G D
Sbjct: 61  NDNLMELLICIDALKRASAKRITAVLPYFGYARQDRKP-GPRTPISAKLVANLITVAGAD 119

Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPI-VVSPDIGGVVRARAIAK 182
           RVL+VDLHA QIQGFFD+P DN++ +P++  D+       PI VVSPD+GGVVRARA+AK
Sbjct: 120 RVLSVDLHAGQIQGFFDIPTDNLYAAPVMSADIQARFAGKPITVVSPDVGGVVRARALAK 179

Query: 183 LLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAK 242
            L++  +AI+DKRR R   S+VM+IIGDV GR CVLVDD++D+ GTLC AA ALKE GA 
Sbjct: 180 RLDNAPLAIVDKRRERPGESEVMNIIGDVNGRFCVLVDDIVDSAGTLCNAAAALKEGGAT 239

Query: 243 RVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGMLAEAIRR 302
            V AY TH + SG A   +  S + E+V+ D+I   D  +A   +R LT++ +LAEA+RR
Sbjct: 240 DVVAYCTHGVLSGAAVPRVDKSELAELVITDSIATYDAAEASEKIRILTIAPLLAEAVRR 299

Query: 303 ISNEESISAMFE 314
           I++E S+S++F+
Sbjct: 300 IADESSVSSLFD 311


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: 302
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: 315
Length of database: 311
Length adjustment: 27
Effective length of query: 288
Effective length of database: 284
Effective search space:    81792
Effective search space used:    81792
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 WP_085217580.1 B9N75_RS03680 (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.2178978.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.4e-118  379.1   0.1   7.2e-118  378.9   0.1    1.0  1  NCBI__GCF_900177405.1:WP_085217580.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085217580.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.9   0.1  7.2e-118  7.2e-118       1     309 []       1     311 []       1     311 [] 0.98

  Alignments for each domain:
  == domain 1  score: 378.9 bits;  conditional E-value: 7.2e-118
                             TIGR01251   1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllid 73 
                                           +k+lsg+s++ l e++a +l+++++d++v++Fad+E+ v+i+e+vrg+dvf+i qst  p nd+lmell+ id
  NCBI__GCF_900177405.1:WP_085217580.1   1 MKLLSGNSNRPLVEAIAAYLEMPITDASVRRFADEEVFVEIHENVRGEDVFVI-QSTAFPANDNLMELLICID 72 
                                           799**************************************************.9****************** PP

                             TIGR01251  74 alkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsas 146
                                           alkrasak++tav+Py+gYaRqd+k  +r+pisaklva+l++ aGadrvl vdlH+ qiqgfFd+p +nl+a+
  NCBI__GCF_900177405.1:WP_085217580.1  73 ALKRASAKRITAVLPYFGYARQDRKPGPRTPISAKLVANLITVAGADRVLSVDLHAGQIQGFFDIPTDNLYAA 145
                                           ************************************************************************* PP

                             TIGR01251 147 pklieelkkke.lknlvvvsPDkGaverakkvakklg.lelaiieKeRdskenevevtnllgdvegkdvvivD 217
                                           p++ ++++++   k ++vvsPD G+v ra+++ak+l+ ++lai++K+R+ +  e ev+n++gdv+g+ +v+vD
  NCBI__GCF_900177405.1:WP_085217580.1 146 PVMSADIQARFaGKPITVVSPDVGGVVRARALAKRLDnAPLAIVDKRRE-RPGESEVMNIIGDVNGRFCVLVD 217
                                           *********99899999*******************99***********.777******************** PP

                             TIGR01251 218 DiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kklpkvseisva 288
                                           Di++++gTl++aa +Lke GA++v++++thgv+sg A+ r++++ + e+++t++i++ +  ++ +k++ +++a
  NCBI__GCF_900177405.1:WP_085217580.1 218 DIVDSAGTLCNAAAALKEGGATDVVAYCTHGVLSGAAVPRVDKSELAELVITDSIATyDAaEASEKIRILTIA 290
                                           *********************************************************7668999********* PP

                             TIGR01251 289 pliaeaiarihenesvsslfd 309
                                           pl+aea++ri++++svsslfd
  NCBI__GCF_900177405.1:WP_085217580.1 291 PLLAEAVRRIADESSVSSLFD 311
                                           *******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (311 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: 16.18
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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