GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroB in Sphingomonas koreensis DSMZ 15582

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate Ga0059261_3591 Ga0059261_3591 3-dehydroquinate synthase (EC 4.2.3.4)

Query= BRENDA::P07639
         (362 letters)



>FitnessBrowser__Korea:Ga0059261_3591
          Length = 366

 Score =  273 bits (697), Expect = 7e-78
 Identities = 161/345 (46%), Positives = 212/345 (61%), Gaps = 7/345 (2%)

Query: 1   MERIVVTLGERSYPITIASGLFNEPASFL-PLKSGEQVMLVTNETLAPLYLDKVRGVLEQ 59
           M  + V LG RSY + I SGL    A  L P       ++VT+  +AP + +++   L  
Sbjct: 1   MRTVPVALGARSYEVRIESGLLGRAAEQLAPFVRKRPFVIVTDANVAP-HGERLAANLAA 59

Query: 60  AGVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQ 119
           AG+  +++ILP GE  KS   L+++   LL     R   ++ALGGGV+GDL GFA+A  +
Sbjct: 60  AGIASETIILPPGEGTKSWTQLESLLDRLLDLGIERGDHVIALGGGVIGDLVGFASAILK 119

Query: 120 RGVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELA 179
           RG  F+Q+PTTLL+QVDSSVGGKTA+N   GKN++GAF+QP+ V++D D L TLP RE  
Sbjct: 120 RGCNFVQIPTTLLAQVDSSVGGKTAINARAGKNLVGAFHQPSVVLIDPDLLDTLPLREQR 179

Query: 180 SGLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERE-TG 238
           +G AEV+KYG+I D  FF W E N  ALL  D  A  Y I      KA +VA DERE TG
Sbjct: 180 AGYAEVVKYGLIDDADFFAWCEGNGAALLAGDPNAREYAIAHSVGAKARIVADDERETTG 239

Query: 239 LRALLNLGHTFGHAIEAEMGYGN-WLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLL 297
            RALLNLGHTFGHA+EAE G+ +  LHGE VAAGM +A   S R G   + + +R+   L
Sbjct: 240 RRALLNLGHTFGHALEAETGFSDQLLHGEGVAAGMALAFAFSARQGLCPATDAERVAAHL 299

Query: 298 KRAGLP---VNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIG 339
           K +GLP    +     +    + HML DKK+ AG +  +L   IG
Sbjct: 300 KASGLPHDLASAGIATNGARLVEHMLHDKKMDAGTLPFLLTRGIG 344


Lambda     K      H
   0.320    0.136    0.392 

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: 312
Number of extensions: 12
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: 362
Length of database: 366
Length adjustment: 29
Effective length of query: 333
Effective length of database: 337
Effective search space:   112221
Effective search space used:   112221
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate Ga0059261_3591 Ga0059261_3591 (3-dehydroquinate synthase (EC 4.2.3.4))
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.3782.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-108  348.2   0.0     3e-108  348.0   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_3591  Ga0059261_3591 3-dehydroquinate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3591  Ga0059261_3591 3-dehydroquinate synthase (EC 4.2.3.4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.0   0.0    3e-108    3e-108       1     338 [.      13     356 ..      13     362 .. 0.95

  Alignments for each domain:
  == domain 1  score: 348.0 bits;  conditional E-value: 3e-108
                                 TIGR01357   1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 
                                               y+v +++gll +++e+la   +++  v++td +v+  ++e+l++ l+++g++ +++++p+ge +Ks+++
  lcl|FitnessBrowser__Korea:Ga0059261_3591  13 YEVRIESGLLGRAAEQLAPfvRKRPFVIVTDANVAP-HGERLAANLAAAGIASETIILPPGEGTKSWTQ 80 
                                               6899**************986667888888888887.779999999999******************** PP

                                 TIGR01357  68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136
                                               +++lld+ll+ ++er + ++a+GGGv+gDl+GF+ a+ +RG ++vq+PTtlla+vDssvGGKt+in + 
  lcl|FitnessBrowser__Korea:Ga0059261_3591  81 LESLLDRLLDLGIERGDHVIALGGGVIGDLVGFASAILKRGCNFVQIPTTLLAQVDSSVGGKTAINARA 149
                                               ********************************************************************* PP

                                 TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205
                                               gkNl+Gaf+qP++Vlid+++l tlp re r+G+aEv+K+gli da++f+++e n ++ll   + +a e 
  lcl|FitnessBrowser__Korea:Ga0059261_3591 150 GKNLVGAFHQPSVVLIDPDLLDTLPLREQRAGYAEVVKYGLIDDADFFAWCEGNGAALLAG-DPNAREY 217
                                               *******************************************************999875.55999** PP

                                 TIGR01357 206 likrsievKaevVeeDekes.glRalLNfGHtlgHaiEallkyk..lsHGeaVaiGmvveaklseklgl 271
                                               +i++s+  Ka++V+ De+e+ g RalLN+GHt+gHa+Ea+++++  l HGe Va Gm++++ +s + gl
  lcl|FitnessBrowser__Korea:Ga0059261_3591 218 AIAHSVGAKARIVADDERETtGRRALLNLGHTFGHALEAETGFSdqLLHGEGVAAGMALAFAFSARQGL 286
                                               *******************99********************99889*********************** PP

                                 TIGR01357 272 lkaellerlvallkklglptklkk...klsveellkallkDKKnegskiklvlleeiGkaalasevtee 337
                                               ++a+++er++a lk+ glp +l +    ++   l++++l+DKK++++++ + l + iG ++l+++v   
  lcl|FitnessBrowser__Korea:Ga0059261_3591 287 CPATDAERVAAHLKASGLPHDLASagiATNGARLVEHMLHDKKMDAGTLPFLLTRGIGATYLDKQVNLA 355
                                               ************************99889999******************************9888554 PP

                                 TIGR01357 338 e 338
                                               +
  lcl|FitnessBrowser__Korea:Ga0059261_3591 356 D 356
                                               4 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (366 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: 10.37
//
[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