Alignments for a candidate for aroG in Sulfuricurvum kujiense DSM 16994

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Sulfuricurvum kujiense DSM 16994

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_013460028.1 SULKU_RS05885 3-deoxy-7-phosphoheptulonate synthase class II

Query= BRENDA::P29976
         (525 letters)



>NCBI__GCF_000183725.1:WP_013460028.1
          Length = 448

 Score =  549 bits (1414), Expect = e-161
 Identities = 258/443 (58%), Positives = 342/443 (77%), Gaps = 2/443 (0%)

Query: 75  WTPESWKLKKALQLPDYPNANELESVLKTIEAFPPIVFAGEARNLEERLADAAVGKAFLL 134
           W+  SW+ K   Q P YP+   LE +   +  +PP+VFAGEAR L++ LAD   GKAFLL
Sbjct: 4   WSRSSWREKPIKQQPTYPDTAVLEQIESQLRNYPPLVFAGEARTLKKNLADVCEGKAFLL 63

Query: 135 QGGDCAESFKEFNATNIRDTFRVLLQMSIVLTFGGQVPVIKVGRMAGQFAKPRSDAFEEK 194
           QGGDCAESF EF+A NIRDTF+V++QM++V+TF G VPV+KVGR+ GQFAKPRS   E  
Sbjct: 64  QGGDCAESFSEFHAHNIRDTFKVMMQMAVVMTFAGGVPVVKVGRLGGQFAKPRSSDTETV 123

Query: 195 DGVKLPSYKGDNINGDTFDEKSRIPDPNRMIRAYTQSAATLNLLRAFATGGYAAIQRVTQ 254
           +G+ LPSY+GD ING  F+E +R+PDP+RM++AY QSAATLNLLRAFA+GG A + +V  
Sbjct: 124 EGITLPSYRGDIINGVDFNEAARVPDPHRMVQAYNQSAATLNLLRAFASGGLADLHQVHA 183

Query: 255 WNLDFVEQSEQADRYQELANRVDEALGFMSACGLGTD-HPLMTTTDFYTSHECLLLPYEQ 313
           WNL FV Q+E   +Y +L+ ++D++L FM+ACG+ +D +  +  TDFYTSHE LLL YE+
Sbjct: 184 WNLGFVGQNEMTKKYDDLSRQIDDSLRFMAACGITSDTYRTLRETDFYTSHEALLLNYEE 243

Query: 314 SLTRLDSTSGLYYDCSAHMVWCGERTRQLDGAHVEFLRGIANPLGIKVSNKMDPFELVKL 373
           + TR DS +G +YD S+HM+W G+RTRQLDGAHVEF+RGI NP+G+K    MDP +L++L
Sbjct: 244 AFTRQDSLTGEWYDVSSHMLWIGDRTRQLDGAHVEFMRGIKNPIGVKAGPSMDPEDLIRL 303

Query: 374 VEILNPNNKPGRITVIVRMGAENMRVKLPHLIRAVRRSGQIVTWVCDPMHGNTIKAPCGL 433
            +ILNP+N+ GR+ VIVRMGA+ +   +P LIRA+ R G+ V W CDPMHGNTI +  G 
Sbjct: 304 CDILNPDNEAGRLNVIVRMGADKVADGMPALIRAIEREGKKVVWSCDPMHGNTITSN-GY 362

Query: 434 KTRAFDSILAEVRAFLDVHEQEGSHAGGIHLEMTGQNVTECIGGSRTVTYDDLSSRYHTH 493
           KTR  D++L E++ F  VH+ EG++AGG+HLEMTG+NVTEC+GGS  +T ++L SRYHTH
Sbjct: 363 KTRPVDAVLKEMKQFFQVHKAEGTYAGGVHLEMTGKNVTECLGGSFEITSENLKSRYHTH 422

Query: 494 CDPRLNASQSLELAFIVAERLRK 516
           CDPRLNA QSLELAF++A+ L++
Sbjct: 423 CDPRLNADQSLELAFLIADTLKE 445


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: 633
Number of extensions: 21
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: 525
Length of database: 448
Length adjustment: 34
Effective length of query: 491
Effective length of database: 414
Effective search space:   203274
Effective search space used:   203274
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 WP_013460028.1 SULKU_RS05885 (3-deoxy-7-phosphoheptulonate synthase class II)
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.1830882.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.4e-222  722.2   0.0   1.1e-221  722.0   0.0    1.0  1  NCBI__GCF_000183725.1:WP_013460028.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000183725.1:WP_013460028.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  722.0   0.0  1.1e-221  1.1e-221       1     442 [.       4     446 ..       4     447 .. 0.99

  Alignments for each domain:
  == domain 1  score: 722.0 bits;  conditional E-value: 1.1e-221
                             TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfkeve 73 
                                           ws +swr+kp +q+P+yPd++ le+++++l+++PPlv+age+++lk++la+v +G+afllqgGdcaesf+e++
  NCBI__GCF_000183725.1:WP_013460028.1   4 WSRSSWREKPIKQQPTYPDTAVLEQIESQLRNYPPLVFAGEARTLKKNLADVCEGKAFLLQGGDCAESFSEFH 76 
                                           8899********************************************************************* PP

                             TIGR01358  74 adnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafdeaarvpd 146
                                           a+nird+++v++qmavv+t+++++Pvvkvgr+ Gq+akPrs+++e+ +g+tlpsyrGd+ing +f+eaarvpd
  NCBI__GCF_000183725.1:WP_013460028.1  77 AHNIRDTFKVMMQMAVVMTFAGGVPVVKVGRLGGQFAKPRSSDTETVEGITLPSYRGDIINGVDFNEAARVPD 149
                                           ************************************************************************* PP

                             TIGR01358 147 perlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfmsavgvaeae. 218
                                           p+r+v+ay++saatlnllra++sgG+adl++vh+Wnl fv++ + +++y++l+++id++lrfm a+g+++++ 
  NCBI__GCF_000183725.1:WP_013460028.1 150 PHRMVQAYNQSAATLNLLRAFASGGLADLHQVHAWNLGFVGQNEMTKKYDDLSRQIDDSLRFMAACGITSDTy 222
                                           ********************************************************************99988 PP

                             TIGR01358 219 .alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflrgvknPigikvgpsm 290
                                            +l+++++ytshealll+yeea+tr+ds +g+++d+s+h+lWiG+rtrqldgahvef+rg+knPig+k gpsm
  NCBI__GCF_000183725.1:WP_013460028.1 223 rTLRETDFYTSHEALLLNYEEAFTRQDSLTGEWYDVSSHMLWIGDRTRQLDGAHVEFMRGIKNPIGVKAGPSM 295
                                           89*********************************************************************** PP

                             TIGR01358 291 eadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtdpmhGntleaasGyktrrf 363
                                            +++l++l+++l+P+ne Grl +i+r+Ga+k+a+ +P l++a++++G++vvW +dpmhGnt+ +++Gyktr +
  NCBI__GCF_000183725.1:WP_013460028.1 296 DPEDLIRLCDILNPDNEAGRLNVIVRMGADKVADGMPALIRAIEREGKKVVWSCDPMHGNTI-TSNGYKTRPV 367
                                           *************************************************************8.579******* PP

                             TIGR01358 364 ddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdlasryetacdPrlnaeqslelaflva 436
                                           d++l+e+k+ff+vhkaeGt+ GGvhle+tG++vteclGG+ eit+++l+sry+t+cdPrlna+qslelafl+a
  NCBI__GCF_000183725.1:WP_013460028.1 368 DAVLKEMKQFFQVHKAEGTYAGGVHLEMTGKNVTECLGGSFEITSENLKSRYHTHCDPRLNADQSLELAFLIA 440
                                           ************************************************************************* PP

                             TIGR01358 437 eklrea 442
                                           ++l+ea
  NCBI__GCF_000183725.1:WP_013460028.1 441 DTLKEA 446
                                           **9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (448 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: 17.44
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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