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.3987950.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.39
//
[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:

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:

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:

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:

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