Alignments for a candidate for prs in Polaromonas naphthalenivorans CJ2

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Polaromonas naphthalenivorans CJ2

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_011800310.1 PNAP_RS04470 ribose-phosphate pyrophosphokinase

Query= SwissProt::P0A1V6
         (315 letters)



>NCBI__GCF_000015505.1:WP_011800310.1
          Length = 324

 Score =  402 bits (1034), Expect = e-117
 Identities = 204/313 (65%), Positives = 252/313 (80%), Gaps = 2/313 (0%)

Query: 2   PDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCA 61
           PD  +F GNA P +A  I   L TSLG A VG+FSDGEV+V+I +NVR  D+F++QSTCA
Sbjct: 4   PDFLVFTGNANPSMAAEITQHLGTSLGVAHVGQFSDGEVTVEIQQNVRTRDVFVVQSTCA 63

Query: 62  PTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVG 121
           PTNDNLMEL+VMVDAL+RASA RITAVIPYFGYARQDRR RSARVPITAKVVA+ L +VG
Sbjct: 64  PTNDNLMELLVMVDALKRASAERITAVIPYFGYARQDRRPRSARVPITAKVVANMLQAVG 123

Query: 122 VDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIA 181
           V  VLT+DLHA+QIQGFFD+PVDN++ SPILL D+ Q    + +VVSPD+GGVVRARA+A
Sbjct: 124 VTSVLTMDLHADQIQGFFDIPVDNIYASPILLGDLRQRKYTDLMVVSPDVGGVVRARALA 183

Query: 182 KLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGA 241
           K L   DMAIIDKRRP+ANVS+VMH+IGD+ GR+CV++DDMIDT GTL KAAE LKERGA
Sbjct: 184 KQLG-CDMAIIDKRRPKANVSEVMHVIGDIEGRNCVIMDDMIDTAGTLVKAAEVLKERGA 242

Query: 242 KRVFAYATHPIFSGNAANNL-RNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGMLAEAI 300
           K+V+AY THPIFSG A + +     +DEVVV +TIPL    +A   +R L+++ ++AE I
Sbjct: 243 KKVYAYCTHPIFSGPAIDRITHGDALDEVVVTNTIPLNPNAQACKKIRQLSVAPLIAETI 302

Query: 301 RRISNEESISAMF 313
           +RI+  ES+ ++F
Sbjct: 303 QRIAKGESVMSLF 315


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: 333
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: 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 WP_011800310.1 PNAP_RS04470 (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.23317.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-127  410.4   1.3   2.2e-127  410.2   1.3    1.0  1  lcl|NCBI__GCF_000015505.1:WP_011800310.1  PNAP_RS04470 ribose-phosphate py


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015505.1:WP_011800310.1  PNAP_RS04470 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.2   1.3  2.2e-127  2.2e-127       3     309 .]       8     316 ..       6     316 .. 0.98

  Alignments for each domain:
  == domain 1  score: 410.2 bits;  conditional E-value: 2.2e-127
                                 TIGR01251   3 ilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellll 71 
                                               ++ g++++++a+++ ++lg++lg ++v +F+dgE+ v+i+++vr +dvf++ qst+ap+nd+lmell++
  lcl|NCBI__GCF_000015505.1:WP_011800310.1   8 VFTGNANPSMAAEITQHLGTSLGVAHVGQFSDGEVTVEIQQNVRTRDVFVV-QSTCAPTNDNLMELLVM 75 
                                               799************************************************.***************** PP

                                 TIGR01251  72 idalkrasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdvp 139
                                               +dalkrasa+++taviPy+gYaRqd++ +  r pi+ak+va++l+++G+++vlt+dlH++qiqgfFd+p
  lcl|NCBI__GCF_000015505.1:WP_011800310.1  76 VDALKRASAERITAVIPYFGYARQDRRPRsARVPITAKVVANMLQAVGVTSVLTMDLHADQIQGFFDIP 144
                                               **************************97758************************************** PP

                                 TIGR01251 140 venlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdv 208
                                               v+n++asp l+ +l++++ ++l+vvsPD G+v ra+++ak+lg+++aii+K+R+ k+n+ ev++++gd+
  lcl|NCBI__GCF_000015505.1:WP_011800310.1 145 VDNIYASPILLGDLRQRKYTDLMVVSPDVGGVVRARALAKQLGCDMAIIDKRRP-KANVSEVMHVIGDI 212
                                               ******************************************************.899*********** PP

                                 TIGR01251 209 egkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeag.veevivtntilv.e 275
                                               eg+++vi+DD+i+T+gTlvkaae+Lke+GAkkv++++th++fsg+A+ r+++   ++ev+vtnti+   
  lcl|NCBI__GCF_000015505.1:WP_011800310.1 213 EGRNCVIMDDMIDTAGTLVKAAEVLKERGAKKVYAYCTHPIFSGPAIDRITHGDaLDEVVVTNTIPLnP 281
                                               ***************************************************99879***********74 PP

                                 TIGR01251 276 e.kklpkvseisvapliaeaiarihenesvsslfd 309
                                               + ++++k++++svapliae+i ri+++esv slf+
  lcl|NCBI__GCF_000015505.1:WP_011800310.1 282 NaQACKKIRQLSVAPLIAETIQRIAKGESVMSLFS 316
                                               469******************************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 6.96
//
[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