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_RS23245 BPHYT_RS23245 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::Q9K169
         (351 letters)



>FitnessBrowser__BFirm:BPHYT_RS23245
          Length = 372

 Score =  404 bits (1038), Expect = e-117
 Identities = 205/346 (59%), Positives = 255/346 (73%), Gaps = 5/346 (1%)

Query: 8   DDIKIKEVKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHD 67
           DD++I  V+ L+ P     ELP+      LV +TR EI+D++HGRD RL++I+GPCSIHD
Sbjct: 26  DDVRIGAVRPLISPALLQDELPVPPSVQTLVEKTRAEIADILHGRDDRLVMIVGPCSIHD 85

Query: 68  PKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQ 127
              A+EYA +L      Y+++LLIVMRVYFEKPRTTVGWKG INDP LDG+F IN GLR 
Sbjct: 86  HDQAIEYAHKLKVAADTYKDDLLIVMRVYFEKPRTTVGWKGYINDPRLDGSFRINEGLRL 145

Query: 128 ARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGF 187
           AR LLL +N +G+  +TEFLD+++PQY ADLI+WGAIGARTTESQ HR+LASGLSCP+GF
Sbjct: 146 ARQLLLDINGLGLATATEFLDLLSPQYIADLIAWGAIGARTTESQSHRQLASGLSCPIGF 205

Query: 188 KNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGGKE-PNYDAE 246
           KNGTDG ++IA DAI AA  SH F+ +TK G +AI  T GN D HVILRGGK+ PNYD+ 
Sbjct: 206 KNGTDGGVQIAADAIVAARASHAFMGMTKMGMAAIFETRGNDDAHVILRGGKKGPNYDSA 265

Query: 247 HVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESH 306
            V    E L++AG+ +++M+DCSHANS K + RQ+EV QD+  QL Q    I+GVM+ESH
Sbjct: 266 SVEATCEALKSAGLREQVMVDCSHANSGKSHLRQLEVVQDLTQQLSQRERRIIGVMLESH 325

Query: 307 LVEGRQD-KPEV---YGKSITDACIGWGATEELLALLAGANKKRMA 348
           L EGRQD KP V   +G SITDAC+ W  TE  L  LA A +KR A
Sbjct: 326 LEEGRQDLKPGVPLRHGVSITDACVSWTQTEPALETLAEATRKRRA 371


Lambda     K      H
   0.318    0.135    0.396 

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: 380
Number of extensions: 13
Number of successful extensions: 3
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: 351
Length of database: 372
Length adjustment: 29
Effective length of query: 322
Effective length of database: 343
Effective search space:   110446
Effective search space used:   110446
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_RS23245 BPHYT_RS23245 (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.22530.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.7e-156  506.2   0.0     2e-156  506.0   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS23245  BPHYT_RS23245 phospho-2-dehydro-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS23245  BPHYT_RS23245 phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  506.0   0.0    2e-156    2e-156       1     342 []      26     370 ..      26     370 .. 0.99

  Alignments for each domain:
  == domain 1  score: 506.0 bits;  conditional E-value: 2e-156
                                TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakr 70 
                                              dd+ri ++ +l++P+ l+ + p+ +++++ v+k+r eiadil+G+ddrl++++GPcsihd   a+eya++
  lcl|FitnessBrowser__BFirm:BPHYT_RS23245  26 DDVRIGAVRPLISPALLQDELPVPPSVQTLVEKTRAEIADILHGRDDRLVMIVGPCSIHDHDQAIEYAHK 95 
                                              799******************************************************************* PP

                                TIGR00034  71 lkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatell 140
                                              lk  a+ +kddl ivmrvyfekPrttvGWkG indP l++sf++n+Glr+ar+llld++ lgl +ate+l
  lcl|FitnessBrowser__BFirm:BPHYT_RS23245  96 LKVAADTYKDDLLIVMRVYFEKPRTTVGWKGYINDPRLDGSFRINEGLRLARQLLLDINGLGLATATEFL 165
                                              ********************************************************************** PP

                                TIGR00034 141 dtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtka 210
                                              d  spqy+adl++wgaiGarttesq hr+lasgls+p+gfkngtdG++++a dai aa+a+h f+++tk 
  lcl|FitnessBrowser__BFirm:BPHYT_RS23245 166 DLLSPQYIADLIAWGAIGARTTESQSHRQLASGLSCPIGFKNGTDGGVQIAADAIVAARASHAFMGMTKM 235
                                              ********************************************************************** PP

                                TIGR00034 211 GqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaes 279
                                              G +ai et+Gn+d+h+ilrGGkk pnyd+++v++++e l+ agl+e++m+d+sh+ns k + rqlev+++
  lcl|FitnessBrowser__BFirm:BPHYT_RS23245 236 GMAAIFETRGNDDAHVILRGGKKgPNYDSASVEATCEALKSAGLREQVMVDCSHANSGKSHLRQLEVVQD 305
                                              ********************************************************************** PP

                                TIGR00034 280 vveqiaeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavkerr 342
                                              +++q+++ e+ iiGvm+es+leeG+q+l  + +l +G+s+tdac++w +te  l+ laea ++rr
  lcl|FitnessBrowser__BFirm:BPHYT_RS23245 306 LTQQLSQRERRIIGVMLESHLEEGRQDLkpGVPLRHGVSITDACVSWTQTEPALETLAEATRKRR 370
                                              ****************************656789**************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (372 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.77
//
[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