Alignments for a candidate for aroG in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Burkholderia phytofirmans PsJN

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate BPHYT_RS03535 BPHYT_RS03535 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::C3TIE2
         (350 letters)



>FitnessBrowser__BFirm:BPHYT_RS03535
          Length = 357

 Score =  473 bits (1216), Expect = e-138
 Identities = 231/347 (66%), Positives = 279/347 (80%)

Query: 3   YQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCS 62
           +  DD+RI+E+KEL PP  L+ +F   E  ++ + ++R A+H+IL G +DRL+V+IGPCS
Sbjct: 4   HNTDDVRIRELKELTPPAHLIREFACDETVSDVIYNSRTAMHRILHGMEDRLIVIIGPCS 63

Query: 63  IHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDG 122
           IHD  AA EYA RL+  R+    ELEIVMRVYFEKPRTTVGWKGLINDPHMDNSF+INDG
Sbjct: 64  IHDTKAAMEYAGRLIEQRKRFAGELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFKINDG 123

Query: 123 LRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCP 182
           LR AR+LLL IN+ GLPA  E+LDMI+PQY+ADL+SWGAIGARTTESQVHRELASGLSCP
Sbjct: 124 LRTARELLLRINELGLPAGTEYLDMISPQYIADLISWGAIGARTTESQVHRELASGLSCP 183

Query: 183 VGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYS 242
           VGFKNGTDG +K+A+DAI AA  PH FLSVTK GHSAIV+T+GN DCHIILRGGK PNY 
Sbjct: 184 VGFKNGTDGNVKIAVDAIKAASQPHHFLSVTKGGHSAIVSTAGNEDCHIILRGGKTPNYD 243

Query: 243 AKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVE 302
           A  V      + KAGL A++MID SHANSSK+ + Q+ VCAD+ +QIA G++ I+GVMVE
Sbjct: 244 ADSVNAACADIGKAGLAARLMIDASHANSSKKHENQIPVCADIGRQIASGDERIVGVMVE 303

Query: 303 SHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349
           SHLV G Q L+ G  L YG+SITDACIGW+++ A+L  LA+AVK RR
Sbjct: 304 SHLVAGRQDLQEGCALTYGQSITDACIGWDESVAVLEGLADAVKQRR 350


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: 466
Number of extensions: 9
Number of successful extensions: 1
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: 357
Length adjustment: 29
Effective length of query: 321
Effective length of database: 328
Effective search space:   105288
Effective search space used:   105288
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 BPHYT_RS03535 BPHYT_RS03535 (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.31918.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.3e-167  542.8   0.1   1.4e-167  542.6   0.1    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS03535  BPHYT_RS03535 phospho-2-dehydro-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS03535  BPHYT_RS03535 phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  542.6   0.1  1.4e-167  1.4e-167       1     342 []       7     350 ..       7     350 .. 0.99

  Alignments for each domain:
  == domain 1  score: 542.6 bits;  conditional E-value: 1.4e-167
                                TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakr 70 
                                              dd+ri +++el++P++l+++f+  e++ + + +sr+++++il+G +drl+v+iGPcsihd +aa+eya r
  lcl|FitnessBrowser__BFirm:BPHYT_RS03535   7 DDVRIRELKELTPPAHLIREFACDETVSDVIYNSRTAMHRILHGMEDRLIVIIGPCSIHDTKAAMEYAGR 76 
                                              799******************************************************************* PP

                                TIGR00034  71 lkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatell 140
                                              l + ++++  +leivmrvyfekPrttvGWkGlindP++++sf++n+Glr ar+lll ++elglp++te+l
  lcl|FitnessBrowser__BFirm:BPHYT_RS03535  77 LIEQRKRFAGELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFKINDGLRTARELLLRINELGLPAGTEYL 146
                                              ********************************************************************** PP

                                TIGR00034 141 dtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtka 210
                                              d+ispqy+adl+swgaiGarttesqvhrelasgls+pvgfkngtdG++k+a+dai+aa+++h+flsvtk 
  lcl|FitnessBrowser__BFirm:BPHYT_RS03535 147 DMISPQYIADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNVKIAVDAIKAASQPHHFLSVTKG 216
                                              ********************************************************************** PP

                                TIGR00034 211 GqvaivetkGnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesv 280
                                              G++aiv+t+Gned+hiilrGGk+pnyda++v+++++++ kagl ++lmid+sh+ns+k++++q+ v++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS03535 217 GHSAIVSTAGNEDCHIILRGGKTPNYDADSVNAACADIGKAGLAARLMIDASHANSSKKHENQIPVCADI 286
                                              ********************************************************************** PP

                                TIGR00034 281 veqiaeGekaiiGvmiesnleeGnqslke..elkyGksvtdacigwedteallrklaeavkerr 342
                                               +qia+G++ i+Gvm+es+l+ G+q+l+e  +l+yG+s+tdacigw+++ a+l+ la+avk+rr
  lcl|FitnessBrowser__BFirm:BPHYT_RS03535 287 GRQIASGDERIVGVMVESHLVAGRQDLQEgcALTYGQSITDACIGWDESVAVLEGLADAVKQRR 350
                                              ***************************7622699***************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (357 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: 10.20
//
[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