Alignments for a candidate for aroG in Rhodospirillum rubrum ATCC 11170

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Rhodospirillum rubrum ATCC 11170

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate YP_425774.1 Rru_A0683 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::P29976
         (525 letters)



>NCBI__GCF_000013085.1:YP_425774.1
          Length = 461

 Score =  570 bits (1470), Expect = e-167
 Identities = 276/448 (61%), Positives = 336/448 (75%), Gaps = 1/448 (0%)

Query: 72  ALKWTPESWKLKKALQLPDYPNANELESVLKTIEAFPPIVFAGEARNLEERLADAAVGKA 131
           A  WTPESW+ K   Q+PDYP+A  L  V   +  +PP+VFAGEAR+L   LA  + GK 
Sbjct: 2   ATPWTPESWRAKPIDQVPDYPDAARLTDVEAELAKYPPLVFAGEARSLRAALAQVSQGKG 61

Query: 132 FLLQGGDCAESFKEFNATNIRDTFRVLLQMSIVLTFGGQVPVIKVGRMAGQFAKPRSDAF 191
           FLLQGGDCAESF EF+A  IRDTFRV+LQM++VLT+G  +PV+KVGRMAGQFAKPRS   
Sbjct: 62  FLLQGGDCAESFAEFSANTIRDTFRVMLQMAVVLTYGAALPVVKVGRMAGQFAKPRSAPL 121

Query: 192 EEKDGVKLPSYKGDNINGDTFDEKSRIPDPNRMIRAYTQSAATLNLLRAFATGGYAAIQR 251
           E  DGV LPSY+GD +NG  F+E  RIPDP R++R Y QSA+TLNLLRAFA GGYA + +
Sbjct: 122 ETIDGVALPSYRGDMVNGMEFEEGVRIPDPERLLRVYNQSASTLNLLRAFAQGGYADLTQ 181

Query: 252 VTQWNLDFVEQSEQADRYQELANRVDEALGFMSACGLGTDH-PLMTTTDFYTSHECLLLP 310
           V QWNLDFVE S Q++RY+  A+R+ E + FM ACG+  +  P M  TDFYTSHE LLL 
Sbjct: 182 VHQWNLDFVEGSPQSERYRAFADRIAETIEFMRACGITPESVPQMRETDFYTSHEALLLN 241

Query: 311 YEQSLTRLDSTSGLYYDCSAHMVWCGERTRQLDGAHVEFLRGIANPLGIKVSNKMDPFEL 370
           YEQ+LTR+DST+G +YDCSAH++W G+RTR   GAHVEFLRG+ANP+G+K    M P  L
Sbjct: 242 YEQALTRIDSTTGKWYDCSAHLLWIGDRTRDPQGAHVEFLRGVANPVGVKAGPSMSPDGL 301

Query: 371 VKLVEILNPNNKPGRITVIVRMGAENMRVKLPHLIRAVRRSGQIVTWVCDPMHGNTIKAP 430
           ++L ++LNP N+PGR++VIVRMGA  +   LP LIRA+ R G+ V W CDPMHGNT+KA 
Sbjct: 302 LELCDLLNPLNEPGRLSVIVRMGAGKVEAGLPPLIRAIEREGRKVVWSCDPMHGNTMKAG 361

Query: 431 CGLKTRAFDSILAEVRAFLDVHEQEGSHAGGIHLEMTGQNVTECIGGSRTVTYDDLSSRY 490
            G KTR F  IL EV  F  VH  EG+HAGG+H EMTG +VTECIGG+R VT   L  RY
Sbjct: 362 SGFKTRDFKKILQEVTEFFAVHRAEGTHAGGVHFEMTGADVTECIGGARAVTEASLGDRY 421

Query: 491 HTHCDPRLNASQSLELAFIVAERLRKRR 518
           HTHCDPRLNA Q+LELAF++AE L+  R
Sbjct: 422 HTHCDPRLNAHQALELAFLIAESLKTER 449


Lambda     K      H
   0.318    0.132    0.389 

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: 17
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: 525
Length of database: 461
Length adjustment: 34
Effective length of query: 491
Effective length of database: 427
Effective search space:   209657
Effective search space used:   209657
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: 52 (24.6 bits)

Align candidate YP_425774.1 Rru_A0683 (3-deoxy-7-phosphoheptulonate synthase)
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.14563.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   2.7e-223  727.2   0.0   3.2e-223  727.0   0.0    1.0  1  lcl|NCBI__GCF_000013085.1:YP_425774.1  Rru_A0683 3-deoxy-7-phosphoheptu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013085.1:YP_425774.1  Rru_A0683 3-deoxy-7-phosphoheptulonate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  727.0   0.0  3.2e-223  3.2e-223       1     442 [.       5     448 ..       5     449 .. 0.99

  Alignments for each domain:
  == domain 1  score: 727.0 bits;  conditional E-value: 3.2e-223
                              TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfkev 72 
                                            w++eswr+kp  q+P+yPda++l+ v+++l+++PPlv+age+++l++ la+v++G++fllqgGdcaesf e+
  lcl|NCBI__GCF_000013085.1:YP_425774.1   5 WTPESWRAKPIDQVPDYPDAARLTDVEAELAKYPPLVFAGEARSLRAALAQVSQGKGFLLQGGDCAESFAEF 76 
                                            89********************************************************************** PP

                              TIGR01358  73 eadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafdeaarv 144
                                            +a++ird++rv+lqmavvltyga lPvvkvgr+aGq+akPrs+p+e+ dgv lpsyrGd++ng++f+e  r+
  lcl|NCBI__GCF_000013085.1:YP_425774.1  77 SANTIRDTFRVMLQMAVVLTYGAALPVVKVGRMAGQFAKPRSAPLETIDGVALPSYRGDMVNGMEFEEGVRI 148
                                            ************************************************************************ PP

                              TIGR01358 145 pdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfmsavgvae 216
                                            pdperl+r+y++sa+tlnllra+++gGyadl++vh+Wnl+fv+ sp+++ry+++a++i e+++fm+a+g+++
  lcl|NCBI__GCF_000013085.1:YP_425774.1 149 PDPERLLRVYNQSASTLNLLRAFAQGGYADLTQVHQWNLDFVEGSPQSERYRAFADRIAETIEFMRACGITP 220
                                            ************************************************************************ PP

                              TIGR01358 217 ae..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflrgvknPigikv 286
                                            ++  +++++++ytshealll+ye+altr ds++g+++d+sahllWiG+rtr   gahveflrgv+nP+g+k 
  lcl|NCBI__GCF_000013085.1:YP_425774.1 221 ESvpQMRETDFYTSHEALLLNYEQALTRIDSTTGKWYDCSAHLLWIGDRTRDPQGAHVEFLRGVANPVGVKA 292
                                            99999******************************************************************* PP

                              TIGR01358 287 gpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtdpmhGntleaasGy 358
                                            gpsm++d ll+l++ l+P nePGrl++i+r+Ga k+   lP+l++a++++Gr+vvW +dpmhGnt++a+sG+
  lcl|NCBI__GCF_000013085.1:YP_425774.1 293 GPSMSPDGLLELCDLLNPLNEPGRLSVIVRMGAGKVEAGLPPLIRAIEREGRKVVWSCDPMHGNTMKAGSGF 364
                                            ************************************************************************ PP

                              TIGR01358 359 ktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdlasryetacdPrlnaeqsle 430
                                            ktr f +il+ev eff+vh+aeGth GGvh e+tG dvtec+GGar++te  l +ry+t+cdPrlna+q+le
  lcl|NCBI__GCF_000013085.1:YP_425774.1 365 KTRDFKKILQEVTEFFAVHRAEGTHAGGVHFEMTGADVTECIGGARAVTEASLGDRYHTHCDPRLNAHQALE 436
                                            ************************************************************************ PP

                              TIGR01358 431 laflvaeklrea 442
                                            lafl+ae l+ +
  lcl|NCBI__GCF_000013085.1:YP_425774.1 437 LAFLIAESLKTE 448
                                            ********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (461 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: 12.24
//
[ok]

This GapMind analysis is from Apr 10 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