Alignments for a candidate for aroG in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Cupriavidus basilensis 4G11

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate RR42_RS05860 RR42_RS05860 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::C3TIE2
         (350 letters)



>FitnessBrowser__Cup4G11:RR42_RS05860
          Length = 359

 Score =  468 bits (1204), Expect = e-136
 Identities = 230/347 (66%), Positives = 279/347 (80%), Gaps = 3/347 (0%)

Query: 6   DDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHD 65
           DDLRI+E+KELLPP  L+ +F  +E A++ +  AR+++H+IL G DDRL+V+IGPCSIHD
Sbjct: 6   DDLRIRELKELLPPAHLIREFGCSEKASDVIYGARQSMHRILHGMDDRLIVIIGPCSIHD 65

Query: 66  PVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRI 125
             AA EYA  L   R+    ELE+VMRVYFEKPRTTVGWKGLINDPHMD SF+INDGLR 
Sbjct: 66  TRAALEYAKLLKVQRDRFAGELEVVMRVYFEKPRTTVGWKGLINDPHMDGSFKINDGLRT 125

Query: 126 ARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGF 185
           AR+LLL+I++ G+P   E+LDMI+PQY+ADL+SWGAIGARTTESQVHRELASGLSCPVGF
Sbjct: 126 ARELLLNISELGVPTGTEYLDMISPQYIADLVSWGAIGARTTESQVHRELASGLSCPVGF 185

Query: 186 KNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKH 245
           KNGTDG +K+A+DAI AA  PH FLSVTK GHSAIV+TSGN DCHIILRGGK PNY A  
Sbjct: 186 KNGTDGNVKIAVDAIKAASQPHHFLSVTKGGHSAIVSTSGNEDCHIILRGGKTPNYDAAS 245

Query: 246 VAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHL 305
           V E  E ++KAGL A++MID SHANSSK+ + Q+ VC D+ +Q+A G++ I+GVMVESHL
Sbjct: 246 VQEACEAISKAGLAARLMIDASHANSSKKHENQIPVCEDIGRQMAAGDERIVGVMVESHL 305

Query: 306 VEGNQSLESGEP---LAYGKSITDACIGWEDTDALLRQLANAVKARR 349
           V G Q    G P   L YG+S+TDACIGW+D+  +L  LA+AVKARR
Sbjct: 306 VGGRQDHAQGTPVEDLTYGQSVTDACIGWDDSVKVLETLASAVKARR 352


Lambda     K      H
   0.317    0.134    0.397 

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: 467
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: 350
Length of database: 359
Length adjustment: 29
Effective length of query: 321
Effective length of database: 330
Effective search space:   105930
Effective search space used:   105930
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate RR42_RS05860 RR42_RS05860 (phospho-2-dehydro-3-deoxyheptonate aldolase)
to HMM TIGR00034 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

# 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/TIGR00034.hmm
# target sequence database:        /tmp/gapView.25103.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00034  [M=342]
Accession:   TIGR00034
Description: aroFGH: 3-deoxy-7-phosphoheptulonate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-166  538.9   0.0   2.2e-166  538.7   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS05860  RR42_RS05860 phospho-2-dehydro-3


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS05860  RR42_RS05860 phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  538.7   0.0  2.2e-166  2.2e-166       1     342 []       6     352 ..       6     352 .. 0.98

  Alignments for each domain:
  == domain 1  score: 538.7 bits;  conditional E-value: 2.2e-166
                                 TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyak 69 
                                               ddlri +++ell+P++l+++f  +eka + +  +r+++++il+G ddrl+v+iGPcsihd +aaleyak
  lcl|FitnessBrowser__Cup4G11:RR42_RS05860   6 DDLRIRELKELLPPAHLIREFGCSEKASDVIYGARQSMHRILHGMDDRLIVIIGPCSIHDTRAALEYAK 74 
                                               799****************************************************************** PP

                                 TIGR00034  70 rlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplate 138
                                                lk  ++++  +le+vmrvyfekPrttvGWkGlindP++++sf++n+Glr ar+lll++ elg+p++te
  lcl|FitnessBrowser__Cup4G11:RR42_RS05860  75 LLKVQRDRFAGELEVVMRVYFEKPRTTVGWKGLINDPHMDGSFKINDGLRTARELLLNISELGVPTGTE 143
                                               ********************************************************************* PP

                                 TIGR00034 139 lldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsv 207
                                               +ld+ispqy+adl+swgaiGarttesqvhrelasgls+pvgfkngtdG++k+a+dai+aa+++h+flsv
  lcl|FitnessBrowser__Cup4G11:RR42_RS05860 144 YLDMISPQYIADLVSWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNVKIAVDAIKAASQPHHFLSV 212
                                               ********************************************************************* PP

                                 TIGR00034 208 tkaGqvaivetkGnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlev 276
                                               tk G++aiv+t+Gned+hiilrGGk+pnyda++v+e++e ++kagl ++lmid+sh+ns+k++++q+ v
  lcl|FitnessBrowser__Cup4G11:RR42_RS05860 213 TKGGHSAIVSTSGNEDCHIILRGGKTPNYDAASVQEACEAISKAGLAARLMIDASHANSSKKHENQIPV 281
                                               ********************************************************************* PP

                                 TIGR00034 277 aesvveqiaeGekaiiGvmiesnleeGnqslk.....eelkyGksvtdacigwedteallrklaeavke 340
                                               +e++ +q+a G++ i+Gvm+es+l++G+q+       e+l+yG+svtdacigw+d+ ++l+ la+avk+
  lcl|FitnessBrowser__Cup4G11:RR42_RS05860 282 CEDIGRQMAAGDERIVGVMVESHLVGGRQDHAqgtpvEDLTYGQSVTDACIGWDDSVKVLETLASAVKA 350
                                               *****************************98512233579****************************9 PP

                                 TIGR00034 341 rr 342
                                               rr
  lcl|FitnessBrowser__Cup4G11:RR42_RS05860 351 RR 352
                                               96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (359 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: 8.33
//
[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