Alignments for a candidate for prs in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Halomonas desiderata SP1

Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate WP_086509887.1 BZY95_RS10555 ribose-phosphate pyrophosphokinase

Query= BRENDA::P0A719
         (315 letters)



>NCBI__GCF_002151265.1:WP_086509887.1
          Length = 309

 Score =  448 bits (1152), Expect = e-131
 Identities = 223/308 (72%), Positives = 267/308 (86%), Gaps = 1/308 (0%)

Query: 6   LFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPTND 65
           +FAGNA PELAQ+IA  L T +G+A VG+FSDGE++V+INENVRG D+FI+QSTCAPTND
Sbjct: 2   VFAGNANPELAQKIAESLDTRMGNATVGQFSDGEIAVEINENVRGKDVFILQSTCAPTND 61

Query: 66  NLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVDRV 125
           NLMEL++MVDALRRASA RITAV+PYFGYARQDRRVRSARVPI+AKVVAD +   GVDRV
Sbjct: 62  NLMELILMVDALRRASATRITAVVPYFGYARQDRRVRSARVPISAKVVADMMVKAGVDRV 121

Query: 126 LTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAKLLN 185
           +T+DLHA+QIQGFFDVPVDNV+GSPILL+D+ + N D+ +VVSPD+GGVVRARAIAK LN
Sbjct: 122 MTMDLHADQIQGFFDVPVDNVYGSPILLDDIERQNYDDLVVVSPDVGGVVRARAIAKQLN 181

Query: 186 DTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAKRVF 245
             D+AIIDKRRP+AN +QVMHIIG++  R CV+VDDMIDT GTLCKA +ALKE GA+RV 
Sbjct: 182 -ADLAIIDKRRPQANQAQVMHIIGEIENRTCVVVDDMIDTAGTLCKAGDALKEHGARRVV 240

Query: 246 AYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAIRRISN 305
           AYATHPI SG A  N+  SV+DEVVV DTIPLSD  +    +R L+++G++AEAIRR+SN
Sbjct: 241 AYATHPILSGPAVENITGSVLDEVVVTDTIPLSDVARRSGKIRQLSVAGLIAEAIRRVSN 300

Query: 306 EESISAMF 313
           EES+SAMF
Sbjct: 301 EESVSAMF 308


Lambda     K      H
   0.321    0.137    0.385 

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: 362
Number of extensions: 8
Number of successful extensions: 2
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: 309
Length adjustment: 27
Effective length of query: 288
Effective length of database: 282
Effective search space:    81216
Effective search space used:    81216
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_086509887.1 BZY95_RS10555 (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.24884.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.1e-128  413.0   4.5   3.4e-128  412.8   4.5    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086509887.1  BZY95_RS10555 ribose-phosphate p


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086509887.1  BZY95_RS10555 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.8   4.5  3.4e-128  3.4e-128       2     308 ..       1     308 [.       1     309 [] 0.98

  Alignments for each domain:
  == domain 1  score: 412.8 bits;  conditional E-value: 3.4e-128
                                 TIGR01251   2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelll 70 
                                               ++++g++++ela+k+a++l++++g+++v +F+dgE+ v+i+e+vrgkdvfi+ qst+ap+nd+lmel+l
  lcl|NCBI__GCF_002151265.1:WP_086509887.1   1 MVFAGNANPELAQKIAESLDTRMGNATVGQFSDGEIAVEINENVRGKDVFIL-QSTCAPTNDNLMELIL 68 
                                               689*************************************************.**************** PP

                                 TIGR01251  71 lidalkrasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdv 138
                                               ++dal+rasa ++tav+Py+gYaRqd++++  r pisak+va+++ +aG+drv+t+dlH++qiqgfFdv
  lcl|NCBI__GCF_002151265.1:WP_086509887.1  69 MVDALRRASATRITAVVPYFGYARQDRRVRsARVPISAKVVADMMVKAGVDRVMTMDLHADQIQGFFDV 137
                                               ****************************9857************************************* PP

                                 TIGR01251 139 pvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgd 207
                                               pv+n+++sp l++++++++ ++lvvvsPD G+v ra+++ak+l+++laii+K+R+ ++n+++v++++g+
  lcl|NCBI__GCF_002151265.1:WP_086509887.1 138 PVDNVYGSPILLDDIERQNYDDLVVVSPDVGGVVRARAIAKQLNADLAIIDKRRP-QANQAQVMHIIGE 205
                                               *******************************************************.888********** PP

                                 TIGR01251 208 vegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilvee 276
                                               +e++++v+vDD+i+T+gTl+ka ++Lke+GA++v+++ath+++sg+A+e+++ ++++ev+vt+ti+ ++
  lcl|NCBI__GCF_002151265.1:WP_086509887.1 206 IENRTCVVVDDMIDTAGTLCKAGDALKEHGARRVVAYATHPILSGPAVENITGSVLDEVVVTDTIPLSD 274
                                               *******************************************************************55 PP

                                 TIGR01251 277 ..kklpkvseisvapliaeaiarihenesvsslf 308
                                                 ++  k++++sva liaeai+r++++esvs++f
  lcl|NCBI__GCF_002151265.1:WP_086509887.1 275 vaRRSGKIRQLSVAGLIAEAIRRVSNEESVSAMF 308
                                               5899*****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (309 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: 00:00:00.01
# Mc/sec: 9.29
//
[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