GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Dinoroseobacter shibae DFL-12

Align Phospho-2-dehydro-3-deoxyheptonate aldolase 2, chloroplastic; 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 2; DAHP synthase 2; PhDAHP2; Phospho-2-keto-3-deoxyheptonate aldolase 2; EC 2.5.1.54 (characterized)
to candidate 3608121 Dshi_1526 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)

Query= SwissProt::A0A067XGX8
         (512 letters)



>FitnessBrowser__Dino:3608121
          Length = 458

 Score =  514 bits (1325), Expect = e-150
 Identities = 252/448 (56%), Positives = 327/448 (72%), Gaps = 2/448 (0%)

Query: 59  TTKWNLESWKTKPAFQLPDYPDKVELESVLKTLSTYPPIVFAGEARNLEEKLGEAALGNA 118
           T  W+   W+TKP  Q+P+Y D   L +V   L+ YPP+VFAGEAR+L  +L + A G  
Sbjct: 2   TKAWSKSDWRTKPRIQMPEYMDPAALAAVEARLTQYPPLVFAGEARSLRRELADVANGKG 61

Query: 119 FLLQGGDCAESFKEFSANNIRDTFRVMLQMGVVLMFGGQMPVIKVGRMAGQFAKPRSDPF 178
           FLLQGGDCAESF EF A+ IRDTF+VMLQM +VL +G ++PV+KVGRMAGQFAKPRS P 
Sbjct: 62  FLLQGGDCAESFGEFGADLIRDTFKVMLQMAMVLTYGAKVPVVKVGRMAGQFAKPRSAPT 121

Query: 179 EEKDGVKLPSYRGDNVNGDAFDEKSRIPDPHRMVRAYTQSVATLNLLRAFASGGYAAMQR 238
           E K+GV+LPSYRGD +N   F  +SRIP+P +M++AYTQ+ ATLNLLRAF+ GGYA + +
Sbjct: 122 EVKEGVELPSYRGDIINDLDFTPESRIPNPEKMLQAYTQAAATLNLLRAFSKGGYADIHQ 181

Query: 239 VNQWNLDFTDQSEQGDRYRELAHRVDEAMGFMTAAGLTVDHTI-MTTTDFWTSHECLLLP 297
           V+ W L FTD+ E  ++YRE+A R+ +A+ FM +AGLT ++   + T DF+TSHE LLL 
Sbjct: 182 VHAWTLGFTDRDE-AEKYREMATRIADALDFMKSAGLTSENNSELATVDFYTSHEALLLE 240

Query: 298 YEQALTREDSTSGLYYDCSAHMIWVGERTRQLDGAHVEFLRGIANPLGIKVSHKMDPDEL 357
           YE+AL R D+T+GL    S HM+W+G+RTRQ DGAHV F  G+ NP+G+K    +  D+L
Sbjct: 241 YEEALCRIDTTTGLPLAGSGHMLWIGDRTRQPDGAHVTFCAGVQNPIGLKCGPSITTDDL 300

Query: 358 VKLIDILNPQNKPGRITVITRMGADNMRVKLPHLIRAVRGAGQIVTWVSDPMHGNTTKAP 417
             L+  LNP+N+ GR+T+I R GA ++   LP L++AV+  G  V W  DPMHGNT K+ 
Sbjct: 301 KVLMARLNPKNEAGRLTLIARFGAGSVGDHLPRLVKAVQEEGANVVWSCDPMHGNTIKSA 360

Query: 418 CGLKTRSFDSIRAELRAFFDVHEQEGSYPGGVHLEMTGQNVTECVGGSRTITYNDLSSRY 477
            G KTR F+S+  E++ FF VH  EG+YPGGVH EMTG++VTEC GG R ++  DLSSRY
Sbjct: 361 SGYKTRPFESVLREVQEFFAVHNAEGTYPGGVHFEMTGKDVTECTGGVRAVSDEDLSSRY 420

Query: 478 HTHCDPRLNASQALELAFAIAERLRRRR 505
           HT CDPRLNASQALELAF +AE +   R
Sbjct: 421 HTACDPRLNASQALELAFLVAEEIETHR 448


Lambda     K      H
   0.319    0.134    0.401 

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: 643
Number of extensions: 18
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: 512
Length of database: 458
Length adjustment: 34
Effective length of query: 478
Effective length of database: 424
Effective search space:   202672
Effective search space used:   202672
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: 52 (24.6 bits)

Align candidate 3608121 Dshi_1526 (phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq))
to HMM TIGR01358 (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/TIGR01358.hmm
# target sequence database:        /tmp/gapView.26370.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01358  [M=443]
Accession:   TIGR01358
Description: DAHP_synth_II: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.3e-207  674.7   0.0   2.7e-207  674.5   0.0    1.0  1  lcl|FitnessBrowser__Dino:3608121  Dshi_1526 phospho-2-dehydro-3-de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608121  Dshi_1526 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  674.5   0.0  2.7e-207  2.7e-207       1     441 [.       5     446 ..       5     448 .. 0.99

  Alignments for each domain:
  == domain 1  score: 674.5 bits;  conditional E-value: 2.7e-207
                         TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfkeveadni 77 
                                       ws++ wr+kp  q+Pey d +al av++ l+++PPlv+age+++l+++la+va+G++fllqgGdcaesf e+ ad i
  lcl|FitnessBrowser__Dino:3608121   5 WSKSDWRTKPRIQMPEYMDPAALAAVEARLTQYPPLVFAGEARSLRRELADVANGKGFLLQGGDCAESFGEFGADLI 81 
                                       78899************************************************************************ PP

                         TIGR01358  78 rdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafdeaarvpdperlvray 154
                                       rd+++v+lqma+vltyga++Pvvkvgr+aGq+akPrs+p+e+k+gv+lpsyrGd+in  +f+ ++r+p+pe++++ay
  lcl|FitnessBrowser__Dino:3608121  82 RDTFKVMLQMAMVLTYGAKVPVVKVGRMAGQFAKPRSAPTEVKEGVELPSYRGDIINDLDFTPESRIPNPEKMLQAY 158
                                       ***************************************************************************** PP

                         TIGR01358 155 aksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfmsavgvaeae..alkrvelytsh 229
                                       +++aatlnllra+ +gGyad+++vh+W+l f+ +  ++++y+++a++i +al fm+++g+++++  +l +v++ytsh
  lcl|FitnessBrowser__Dino:3608121 159 TQAAATLNLLRAFSKGGYADIHQVHAWTLGFTDRD-EAEKYREMATRIADALDFMKSAGLTSENnsELATVDFYTSH 234
                                       *******************************9875.6799********************9988789********** PP

                         TIGR01358 230 eallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflrgvknPigikvgpsmeadellklievldPen 306
                                       ealll+yeeal r d ++g     s+h+lWiG+rtrq dgahv f +gv+nPig+k+gps+++d+l  l+ +l+P+n
  lcl|FitnessBrowser__Dino:3608121 235 EALLLEYEEALCRIDTTTGLPLAGSGHMLWIGDRTRQPDGAHVTFCAGVQNPIGLKCGPSITTDDLKVLMARLNPKN 311
                                       ***************************************************************************** PP

                         TIGR01358 307 ePGrltlisrlGaekiaeklPelleavkaaGravvWvtdpmhGntleaasGyktrrfddilsevkeffevhkaeGth 383
                                       e Grltli+r+Ga  + ++lP+l++av+++G++vvW +dpmhGnt+++asGyktr f+++l ev+eff+vh+aeGt+
  lcl|FitnessBrowser__Dino:3608121 312 EAGRLTLIARFGAGSVGDHLPRLVKAVQEEGANVVWSCDPMHGNTIKSASGYKTRPFESVLREVQEFFAVHNAEGTY 388
                                       ***************************************************************************** PP

                         TIGR01358 384 pGGvhleltGedvteclGGareitetdlasryetacdPrlnaeqslelaflvaeklre 441
                                       pGGvh e+tG+dvtec+GG r+++++dl+sry+tacdPrlna+q+lelaflvae +  
  lcl|FitnessBrowser__Dino:3608121 389 PGGVHFEMTGKDVTECTGGVRAVSDEDLSSRYHTACDPRLNASQALELAFLVAEEIET 446
                                       *****************************************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (458 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: 11.58
//
[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