Alignments for a candidate for prs in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Pseudomonas fluorescens GW456-L13

Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate PfGW456L13_1577 Ribose-phosphate pyrophosphokinase (EC 2.7.6.1)

Query= BRENDA::P0A719
         (315 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1577
          Length = 313

 Score =  424 bits (1091), Expect = e-123
 Identities = 209/310 (67%), Positives = 257/310 (82%), Gaps = 1/310 (0%)

Query: 4   MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63
           M +F GNA P+LA+R+  +L+  LGD +VG+FSDGE++ +INENVRG D+FIIQ TCAPT
Sbjct: 4   MMVFTGNANPDLARRVVRQLHIPLGDISVGKFSDGEITAEINENVRGKDVFIIQPTCAPT 63

Query: 64  NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123
           NDNLMELVVM DA RR+SA RITAVIPYFGYARQDRR RSARV I+AKVVAD L+ VG+D
Sbjct: 64  NDNLMELVVMADAFRRSSATRITAVIPYFGYARQDRRPRSARVAISAKVVADMLTVVGID 123

Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAKL 183
           RVLTVDLHA+QIQGFFD+PVDN++GSP+L++D+     +N ++VSPDIGGVVRARA+AK 
Sbjct: 124 RVLTVDLHADQIQGFFDIPVDNIYGSPVLVDDIEDQRFENLMIVSPDIGGVVRARAVAKS 183

Query: 184 LNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAKR 243
           L   D+ IIDKRR +AN S+VMHIIGDV GR C+LVDDM+DT GTLC AA+ALKE GA +
Sbjct: 184 LG-VDLGIIDKRREKANHSEVMHIIGDVEGRTCILVDDMVDTAGTLCHAAKALKEHGAAK 242

Query: 244 VFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAIRRI 303
           VFAY THP+ SG A  N+ NSV+DE+VV +TIPLS   ++   +R L ++ ++AEA+RRI
Sbjct: 243 VFAYCTHPVLSGRAIENIENSVLDELVVTNTIPLSAAAQACARIRQLDIAPVVAEAVRRI 302

Query: 304 SNEESISAMF 313
           SNEESISAMF
Sbjct: 303 SNEESISAMF 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: 359
Number of extensions: 11
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 PfGW456L13_1577 (Ribose-phosphate pyrophosphokinase (EC 2.7.6.1))
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.13902.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   9.5e-127  408.1   2.8   1.1e-126  407.9   2.8    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1577  Ribose-phosphate pyrophosphokina


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1577  Ribose-phosphate pyrophosphokinase (EC 2.7.6.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.9   2.8  1.1e-126  1.1e-126       1     309 []       4     313 .]       4     313 .] 0.98

  Alignments for each domain:
  == domain 1  score: 407.9 bits;  conditional E-value: 1.1e-126
                                               TIGR01251   1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivq 55 
                                                             ++++ g+++++la++v ++l+++lgd++v kF+dgE+  +i+e+vrgkdvfii q
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1577   4 MMVFTGNANPDLARRVVRQLHIPLGDISVGKFSDGEITAEINENVRGKDVFII-Q 57 
                                                             799**************************************************.* PP

                                               TIGR01251  56 stsapvndalmellllidalkrasaksvtaviPyygYaRqdkkak.srepisakl 109
                                                              t+ap+nd+lmel++++da++r+sa ++taviPy+gYaRqd++ +  r +isak+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1577  58 PTCAPTNDNLMELVVMADAFRRSSATRITAVIPYFGYARQDRRPRsARVAISAKV 112
                                                             ******************************************97758******** PP

                                               TIGR01251 110 vaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspklieelkkkelknlvvv 164
                                                             va++l+ +G+drvltvdlH++qiqgfFd+pv+n+++sp+l+++++++  +nl++v
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1577 113 VADMLTVVGIDRVLTVDLHADQIQGFFDIPVDNIYGSPVLVDDIEDQRFENLMIV 167
                                                             ******************************************************* PP

                                               TIGR01251 165 sPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDDi 219
                                                             sPD G+v ra++vak+lg++l ii+K+R+ k+n+ ev++++gdveg+++++vDD+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1577 168 SPDIGGVVRARAVAKSLGVDLGIIDKRRE-KANHSEVMHIIGDVEGRTCILVDDM 221
                                                             *****************************.899********************** PP

                                               TIGR01251 220 isTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv 274
                                                             ++T+gTl++aa++Lke+GA kv++++th+v+sg+A+e++++++++e++vtnti+ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1577 222 VDTAGTLCHAAKALKEHGAAKVFAYCTHPVLSGRAIENIENSVLDELVVTNTIPL 276
                                                             ******************************************************* PP

                                               TIGR01251 275 .ee.kklpkvseisvapliaeaiarihenesvsslfd 309
                                                                 +++ +++++++ap++aea++ri+++es+s++f+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1577 277 sAAaQACARIRQLDIAPVVAEAVRRISNEESISAMFR 313
                                                             65579******************************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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.82
//
[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