Alignments for a candidate for prs in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Herbaspirillum seropedicae SmR1

Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate HSERO_RS19570 HSERO_RS19570 ribose-phosphate pyrophosphokinase

Query= BRENDA::P0A719
         (315 letters)



>FitnessBrowser__HerbieS:HSERO_RS19570
          Length = 316

 Score =  405 bits (1040), Expect = e-118
 Identities = 199/313 (63%), Positives = 254/313 (81%), Gaps = 1/313 (0%)

Query: 1   MPDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTC 60
           + ++ +F GNA PELA+ +A +L   LG A V +FSDGEV V+INENVRG D+F++QSTC
Sbjct: 3   LENLMVFTGNANPELARGVAEKLGIPLGKANVSKFSDGEVMVEINENVRGKDVFVLQSTC 62

Query: 61  APTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV 120
           APTNDNLME+++MVDAL+RASAGRITA IPY+GYARQDRR RSARV I+AKVVA+ L   
Sbjct: 63  APTNDNLMEIMIMVDALKRASAGRITAAIPYYGYARQDRRPRSARVAISAKVVANMLQEA 122

Query: 121 GVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAI 180
           GV+RVL +DLHA+QIQGFFD+PVDN++ SPILL D++  N ++ +VVSPD+GGVVRARA+
Sbjct: 123 GVERVLIMDLHADQIQGFFDIPVDNIYASPILLGDLVNKNYEDLLVVSPDVGGVVRARAL 182

Query: 181 AKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERG 240
           AK LN  D+AIIDKRRP+ANVS+VM+IIG+V GR+CV++DDM+DT GTL KAAE LKERG
Sbjct: 183 AKRLN-CDLAIIDKRRPKANVSEVMNIIGEVEGRNCVIMDDMVDTAGTLTKAAEVLKERG 241

Query: 241 AKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAI 300
           AK+V AY THP+ SG A   + NS +DE+VV DTIPLS   +  P VR LT + +LAE  
Sbjct: 242 AKKVVAYCTHPVLSGPAIERIANSPLDELVVTDTIPLSPAARGCPKVRQLTCADLLAETF 301

Query: 301 RRISNEESISAMF 313
           +RI+  +S+ ++F
Sbjct: 302 KRITKGDSVMSLF 314


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: 319
Number of extensions: 9
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: 316
Length adjustment: 27
Effective length of query: 288
Effective length of database: 289
Effective search space:    83232
Effective search space used:    83232
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 HSERO_RS19570 HSERO_RS19570 (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.26457.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.8e-126  407.2   0.1     2e-126  407.1   0.1    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS19570  HSERO_RS19570 ribose-phosphate p


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS19570  HSERO_RS19570 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.1   0.1    2e-126    2e-126       2     308 ..       7     314 ..       6     315 .. 0.98

  Alignments for each domain:
  == domain 1  score: 407.1 bits;  conditional E-value: 2e-126
                                  TIGR01251   2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmell 69 
                                                +++ g++++ela+ va++lg++lg+++v kF+dgE++v+i+e+vrgkdvf++ qst+ap+nd+lme++
  lcl|FitnessBrowser__HerbieS:HSERO_RS19570   7 MVFTGNANPELARGVAEKLGIPLGKANVSKFSDGEVMVEINENVRGKDVFVL-QSTCAPTNDNLMEIM 73 
                                                89**************************************************.*************** PP

                                  TIGR01251  70 llidalkrasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfF 136
                                                +++dalkrasa+++ta iPyygYaRqd++ +  r +isak+va++l+eaG++rvl++dlH++qiqgfF
  lcl|FitnessBrowser__HerbieS:HSERO_RS19570  74 IMVDALKRASAGRITAAIPYYGYARQDRRPRsARVAISAKVVANMLQEAGVERVLIMDLHADQIQGFF 141
                                                ****************************97758*********************************** PP

                                  TIGR01251 137 dvpvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnl 204
                                                d+pv+n++asp l+ +l +k+ ++l+vvsPD G+v ra+++ak+l+++laii+K+R+ k+n+ ev+n+
  lcl|FitnessBrowser__HerbieS:HSERO_RS19570 142 DIPVDNIYASPILLGDLVNKNYEDLLVVSPDVGGVVRARALAKRLNCDLAIIDKRRP-KANVSEVMNI 208
                                                *********************************************************.899******* PP

                                  TIGR01251 205 lgdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtnti 272
                                                +g+veg+++vi+DD+++T+gTl+kaae+Lke+GAkkv++++th+v+sg+A+er+a++ ++e++vt+ti
  lcl|FitnessBrowser__HerbieS:HSERO_RS19570 209 IGEVEGRNCVIMDDMVDTAGTLTKAAEVLKERGAKKVVAYCTHPVLSGPAIERIANSPLDELVVTDTI 276
                                                ******************************************************************** PP

                                  TIGR01251 273 lv.ee.kklpkvseisvapliaeaiarihenesvsslf 308
                                                +     + +pkv++++ a+l+ae+ +ri+++ sv slf
  lcl|FitnessBrowser__HerbieS:HSERO_RS19570 277 PLsPAaRGCPKVRQLTCADLLAETFKRITKGDSVMSLF 314
                                                **644699*****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (316 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.63
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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