Alignments for a candidate for prs in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Pseudomonas stutzeri RCH2

Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate GFF1073 Psest_1106 ribose-phosphate pyrophosphokinase

Query= BRENDA::P0A719
         (315 letters)



>FitnessBrowser__psRCH2:GFF1073
          Length = 329

 Score =  426 bits (1096), Expect = e-124
 Identities = 210/310 (67%), Positives = 258/310 (83%), Gaps = 1/310 (0%)

Query: 4   MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63
           M +F GNA P+LA+R+  +L+  LGDA VG+FSDGE+SV+INENVRG D+F+IQ TCAPT
Sbjct: 20  MMVFTGNANPDLARRVVRQLHIPLGDAYVGKFSDGEISVEINENVRGKDVFLIQPTCAPT 79

Query: 64  NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123
           NDNLMELVV+ DA RR+SA RITAVIPYFGYARQDRR RSARVPI+AKVVAD L  VGV+
Sbjct: 80  NDNLMELVVLADAFRRSSASRITAVIPYFGYARQDRRPRSARVPISAKVVADMLDVVGVN 139

Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAKL 183
           RVLTVDLHA+QIQGFFD+PVDN++GSP+L++D+     +N ++VSPDIGGVVRARA+AK 
Sbjct: 140 RVLTVDLHADQIQGFFDMPVDNIYGSPVLVDDIQAQRFENLMIVSPDIGGVVRARAVAKS 199

Query: 184 LNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAKR 243
           L   D+AIIDKRRP+AN S+VMHIIGD+ GR C+LVDDM+DT GTLC AA+ALK+ GA +
Sbjct: 200 LG-VDLAIIDKRRPKANQSEVMHIIGDIEGRTCILVDDMVDTAGTLCHAAKALKDHGAAK 258

Query: 244 VFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAIRRI 303
           V+AY THPI SG A  N+  SV+DE+VV +TIPLS   +S   +R L ++ ++AEA+RRI
Sbjct: 259 VYAYCTHPILSGRAIENIEGSVLDELVVTNTIPLSAAAQSCTRIRQLDIAPVVAEAVRRI 318

Query: 304 SNEESISAMF 313
           SN ESISAMF
Sbjct: 319 SNAESISAMF 328


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: 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: 329
Length adjustment: 28
Effective length of query: 287
Effective length of database: 301
Effective search space:    86387
Effective search space used:    86387
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 GFF1073 Psest_1106 (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.21695.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   6.2e-126  405.4   0.9     7e-126  405.3   0.9    1.0  1  lcl|FitnessBrowser__psRCH2:GFF1073  Psest_1106 ribose-phosphate pyro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF1073  Psest_1106 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.3   0.9    7e-126    7e-126       1     309 []      20     329 .]      20     329 .] 0.98

  Alignments for each domain:
  == domain 1  score: 405.3 bits;  conditional E-value: 7e-126
                           TIGR01251   1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidal 75 
                                         ++++ g+++++la++v ++l+++lgd+ v kF+dgE++v+i+e+vrgkdvf+i q t+ap+nd+lmel++l+da+
  lcl|FitnessBrowser__psRCH2:GFF1073  20 MMVFTGNANPDLARRVVRQLHIPLGDAYVGKFSDGEISVEINENVRGKDVFLI-QPTCAPTNDNLMELVVLADAF 93 
                                         799**************************************************.********************* PP

                           TIGR01251  76 krasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspkl 149
                                         +r+sa+++taviPy+gYaRqd++ +  r pisak+va++l  +G++rvltvdlH++qiqgfFd+pv+n+++sp+l
  lcl|FitnessBrowser__psRCH2:GFF1073  94 RRSSASRITAVIPYFGYARQDRRPRsARVPISAKVVADMLDVVGVNRVLTVDLHADQIQGFFDMPVDNIYGSPVL 168
                                         **********************97758************************************************ PP

                           TIGR01251 150 ieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDDiisTgg 224
                                         +++++++  +nl++vsPD G+v ra++vak+lg++laii+K+R+ k+n+ ev++++gd+eg+++++vDD+++T+g
  lcl|FitnessBrowser__psRCH2:GFF1073 169 VDDIQAQRFENLMIVSPDIGGVVRARAVAKSLGVDLAIIDKRRP-KANQSEVMHIIGDIEGRTCILVDDMVDTAG 242
                                         ********************************************.899*************************** PP

                           TIGR01251 225 TlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kklpkvseisvapliaeaiar 297
                                         Tl++aa++Lk++GA kv++++th+++sg+A+e+++ ++++e++vtnti+     +++ +++++++ap++aea++r
  lcl|FitnessBrowser__psRCH2:GFF1073 243 TLCHAAKALKDHGAAKVYAYCTHPILSGRAIENIEGSVLDELVVTNTIPLsAAaQSCTRIRQLDIAPVVAEAVRR 317
                                         **************************************************65579******************** PP

                           TIGR01251 298 ihenesvsslfd 309
                                         i++ es+s++f+
  lcl|FitnessBrowser__psRCH2:GFF1073 318 ISNAESISAMFR 329
                                         **********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (329 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: 8.30
//
[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