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

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.9017.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.56
//
[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