Alignments for a candidate for prs in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Pseudomonas putida KT2440

Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate PP_0722 PP_0722 Ribose-phosphate pyrophosphokinase

Query= BRENDA::P0A719
         (315 letters)



>FitnessBrowser__Putida:PP_0722
          Length = 313

 Score =  424 bits (1090), Expect = e-123
 Identities = 208/313 (66%), Positives = 257/313 (82%), Gaps = 1/313 (0%)

Query: 1   MPDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTC 60
           M  M +F GNA P+LA+R+  +L+  LGD +VG+FSDGE+S +INENVRG D+FIIQ TC
Sbjct: 1   MSKMMVFTGNANPDLARRVVRQLHIPLGDVSVGKFSDGEISTEINENVRGKDVFIIQPTC 60

Query: 61  APTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV 120
           APTNDNLMELVVM DA RR+SA RITAVIPYFGYARQDRR RSARV I+AKVVAD L+ V
Sbjct: 61  APTNDNLMELVVMADAFRRSSASRITAVIPYFGYARQDRRPRSARVAISAKVVADMLTVV 120

Query: 121 GVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAI 180
           G+DRVLTVDLHA+QIQGFFD+PVDN++GSP+L++D+     +N ++VSPDIGGVVRARA+
Sbjct: 121 GIDRVLTVDLHADQIQGFFDIPVDNIYGSPVLVDDIEDQRFENLMIVSPDIGGVVRARAV 180

Query: 181 AKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERG 240
           AK L   D+ IIDKRR +AN S+VMHIIGDV GR C+LVDDM+DT GTLC AA+ALKE G
Sbjct: 181 AKSLG-VDLGIIDKRREKANHSEVMHIIGDVEGRTCILVDDMVDTAGTLCHAAKALKEHG 239

Query: 241 AKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAI 300
           A +V+AY THP+ SG A  N+  SV+DE+VV +T+PLS   ++   +R L ++ ++AEA+
Sbjct: 240 AAKVYAYCTHPVLSGRAIENIEKSVLDELVVTNTVPLSAAAQACDRIRQLDIAPVVAEAV 299

Query: 301 RRISNEESISAMF 313
           RRISNEESISAMF
Sbjct: 300 RRISNEESISAMF 312


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: 355
Number of extensions: 10
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: 313
Length adjustment: 27
Effective length of query: 288
Effective length of database: 286
Effective search space:    82368
Effective search space used:    82368
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 PP_0722 PP_0722 (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.18806.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.2e-128  411.8   2.7   8.1e-128  411.6   2.7    1.0  1  lcl|FitnessBrowser__Putida:PP_0722  PP_0722 Ribose-phosphate pyropho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0722  PP_0722 Ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.6   2.7  8.1e-128  8.1e-128       1     309 []       4     313 .]       4     313 .] 0.98

  Alignments for each domain:
  == domain 1  score: 411.6 bits;  conditional E-value: 8.1e-128
                           TIGR01251   1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidal 75 
                                         ++++ g+++++la++v ++l+++lgdv+v kF+dgE++++i+e+vrgkdvfii q t+ap+nd+lmel++++da+
  lcl|FitnessBrowser__Putida:PP_0722   4 MMVFTGNANPDLARRVVRQLHIPLGDVSVGKFSDGEISTEINENVRGKDVFII-QPTCAPTNDNLMELVVMADAF 77 
                                         799**************************************************.********************* PP

                           TIGR01251  76 krasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspkl 149
                                         +r+sa+++taviPy+gYaRqd++ +  r +isak+va++l+ +G+drvltvdlH++qiqgfFd+pv+n+++sp+l
  lcl|FitnessBrowser__Putida:PP_0722  78 RRSSASRITAVIPYFGYARQDRRPRsARVAISAKVVADMLTVVGIDRVLTVDLHADQIQGFFDIPVDNIYGSPVL 152
                                         **********************97758************************************************ PP

                           TIGR01251 150 ieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDDiisTgg 224
                                         +++++++  +nl++vsPD G+v ra++vak+lg++l ii+K+R+ k+n+ ev++++gdveg+++++vDD+++T+g
  lcl|FitnessBrowser__Putida:PP_0722 153 VDDIEDQRFENLMIVSPDIGGVVRARAVAKSLGVDLGIIDKRRE-KANHSEVMHIIGDVEGRTCILVDDMVDTAG 226
                                         ********************************************.899*************************** PP

                           TIGR01251 225 TlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kklpkvseisvapliaeaiar 297
                                         Tl++aa++Lke+GA kv++++th+v+sg+A+e++++++++e++vtnt++     +++++++++++ap++aea++r
  lcl|FitnessBrowser__Putida:PP_0722 227 TLCHAAKALKEHGAAKVYAYCTHPVLSGRAIENIEKSVLDELVVTNTVPLsAAaQACDRIRQLDIAPVVAEAVRR 301
                                         **************************************************65579******************** PP

                           TIGR01251 298 ihenesvsslfd 309
                                         i+++es+s++f+
  lcl|FitnessBrowser__Putida:PP_0722 302 ISNEESISAMFR 313
                                         **********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (313 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.88
//
[ok]

This GapMind analysis is from Apr 09 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