Alignments for a candidate for aroB in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Burkholderia phytofirmans PsJN

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate BPHYT_RS17885 BPHYT_RS17885 3-dehydroquinate synthase

Query= SwissProt::U3KRF2
         (445 letters)



>FitnessBrowser__BFirm:BPHYT_RS17885
          Length = 361

 Score =  380 bits (975), Expect = e-110
 Identities = 193/335 (57%), Positives = 242/335 (72%), Gaps = 3/335 (0%)

Query: 84  VDVDLGDRSYPIYIGSGLLDQPDLLQRHVHGKRVLVVTNSTVAPIYLDKVVGALTNGNPN 143
           V+V+LG+R+YPI+IG+ L+ Q  L   H+ G  V +VTNSTV P+Y DK+  AL      
Sbjct: 7   VNVELGERAYPIHIGTDLIGQTALFAPHIAGSSVTIVTNSTVDPLYGDKLRAALAPLGKQ 66

Query: 144 VSVESVILPDGEKYKNMDTLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASFLRG 203
           VS  +V+LPDGE YKN++TL  +FD  +  R DR+ T +ALGGGVIGDM G+AAA ++RG
Sbjct: 67  VS--TVVLPDGEAYKNLETLNLIFDALLGGRADRKTTLIALGGGVIGDMTGFAAACYMRG 124

Query: 204 VNFIQIPTTVMAQVDSSVGGKTGINHRLGKNLIGAFYQPQCVLIDTDTLNTLPDRELASG 263
           V FIQ+PTT+++QVDSSVGGKTGINH LGKN+IGAFYQPQ V+ D   L TLP RELA+G
Sbjct: 125 VPFIQVPTTLLSQVDSSVGGKTGINHPLGKNMIGAFYQPQAVIADIGALRTLPPRELAAG 184

Query: 264 LAEVVKYGLIRDANFFEWQEKNMPALMARDPSALAYAIKRSCENKAEVVSLDEKESGLRA 323
           +AEV+K G I DA FF W E N+ AL   +P ALA A+KRSCE KA VV+ DE+E GLRA
Sbjct: 185 IAEVIKTGAIADAGFFRWIETNIEALNRCEPEALAEAVKRSCEIKASVVAQDEREGGLRA 244

Query: 324 TLNLGHTFGHAIETGFGYGQWLHGEAVAAGMVMAVDMSYRLGWIDESIVNRAHNILQQAK 383
            LN GHTFGHAIE G GYG+WLHGEAV  GMVMA D+S RLG++DE+   R  +++  A 
Sbjct: 245 ILNFGHTFGHAIEAGLGYGEWLHGEAVGCGMVMAADLSVRLGYLDEAARKRLVDVIVAAH 304

Query: 384 LPTAPPETMTVEMFKSVMAVDKKVADGLLRLILLK 418
           LPT  P  +    +  +M VDKK   G ++ ILLK
Sbjct: 305 LPTRAP-ALGDSRYVELMRVDKKAEAGAIKFILLK 338


Lambda     K      H
   0.318    0.133    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: 428
Number of extensions: 10
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: 445
Length of database: 361
Length adjustment: 31
Effective length of query: 414
Effective length of database: 330
Effective search space:   136620
Effective search space used:   136620
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: 50 (23.9 bits)

Align candidate BPHYT_RS17885 BPHYT_RS17885 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

# 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/TIGR01357.hmm
# target sequence database:        /tmp/gapView.2045.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01357  [M=344]
Accession:   TIGR01357
Description: aroB: 3-dehydroquinate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.7e-123  397.5   0.0   3.1e-123  397.3   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS17885  BPHYT_RS17885 3-dehydroquinate s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS17885  BPHYT_RS17885 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.3   0.0  3.1e-123  3.1e-123       1     340 [.      16     354 ..      16     358 .. 0.96

  Alignments for each domain:
  == domain 1  score: 397.3 bits;  conditional E-value: 3.1e-123
                                TIGR01357   1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletva 69 
                                              y++++g++l+ +++    +   s++ ++t+++v+ l+++kl++al+ lg +v ++v+pdge +K+let++
  lcl|FitnessBrowser__BFirm:BPHYT_RS17885  16 YPIHIGTDLIGQTALFAPHiAGSSVTIVTNSTVDPLYGDKLRAALAPLGKQVSTVVLPDGEAYKNLETLN 85 
                                              6899****999776665554559*********************************************** PP

                                TIGR01357  70 klldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkN 139
                                               + d+ll   ++rk++l+a+GGGv+gD++GF+Aa y+RG++++qvPTtll++vDssvGGKtgin+plgkN
  lcl|FitnessBrowser__BFirm:BPHYT_RS17885  86 LIFDALLGGRADRKTTLIALGGGVIGDMTGFAAACYMRGVPFIQVPTTLLSQVDSSVGGKTGINHPLGKN 155
                                              ********************************************************************** PP

                                TIGR01357 140 liGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikr 209
                                              +iGafyqP+aV+ d+  l+tlp rel++G+aEviK+g+iada +f+++e+n ++l++ +e eal+e++kr
  lcl|FitnessBrowser__BFirm:BPHYT_RS17885 156 MIGAFYQPQAVIADIGALRTLPPRELAAGIAEVIKTGAIADAGFFRWIETNIEALNR-CEPEALAEAVKR 224
                                              ****************************************************98876.788********* PP

                                TIGR01357 210 sievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllkaelle 278
                                              s+e+Ka+vV++De+e glRa+LNfGHt+gHaiEa l+y+ + HGeaV +Gmv++a ls +lg+l++  ++
  lcl|FitnessBrowser__BFirm:BPHYT_RS17885 225 SCEIKASVVAQDEREGGLRAILNFGHTFGHAIEAGLGYGeWLHGEAVGCGMVMAADLSVRLGYLDEAARK 294
                                              ********************************************************************** PP

                                TIGR01357 279 rlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeell 340
                                              rlv+++ +++lpt+ +  l  + +++ +  DKK+e++ ik++ll+++G++ ++ + ++ e++
  lcl|FitnessBrowser__BFirm:BPHYT_RS17885 295 RLVDVIVAAHLPTRAPA-LGDSRYVELMRVDKKAEAGAIKFILLKRFGETLIT-QAPDAEVH 354
                                              ****************7.9999***************************9999.77666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (361 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: 9.82
//
[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