Alignments for a candidate for aroG in Rhodospirillum centenum SW; ATCC 51521

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Rhodospirillum centenum SW; ATCC 51521

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_012566168.1 RC1_RS04520 3-deoxy-7-phosphoheptulonate synthase class II

Query= BRENDA::P29976
         (525 letters)



>NCBI__GCF_000016185.1:WP_012566168.1
          Length = 486

 Score =  586 bits (1511), Expect = e-172
 Identities = 281/476 (59%), Positives = 363/476 (76%), Gaps = 1/476 (0%)

Query: 46  VTAVHAAEPARNAVSVKESVASSSSGALKWTPESWKLKKALQLPDYPNANELESVLKTIE 105
           +T + A+  AR+    + +  ++     +WTPESW+ K A+Q+P YP+  +L++    + 
Sbjct: 1   MTGLAASSGARSGKRCEMATETAMGTGGRWTPESWRAKPAMQMPTYPDPAKLQAAAARLA 60

Query: 106 AFPPIVFAGEARNLEERLADAAVGKAFLLQGGDCAESFKEFNATNIRDTFRVLLQMSIVL 165
            +PP+VFAGEAR+L+E L  A  G+AFLLQGGDCAESF EF+  NIRDTFRVLLQM+IVL
Sbjct: 61  GYPPLVFAGEARSLKECLGRATQGQAFLLQGGDCAESFSEFHPNNIRDTFRVLLQMAIVL 120

Query: 166 TFGGQVPVIKVGRMAGQFAKPRSDAFEEKDGVKLPSYKGDNINGDTFDEKSRIPDPNRMI 225
           TFGG  PV+KVGRMAGQFAKPRS   E  DGV+LP+Y+GD ING  F  ++R+PDP+RM+
Sbjct: 121 TFGGATPVVKVGRMAGQFAKPRSADMEVVDGVELPAYRGDIINGFDFTPEARVPDPDRMV 180

Query: 226 RAYTQSAATLNLLRAFATGGYAAIQRVTQWNLDFVEQSEQADRYQELANRVDEALGFMSA 285
           +AY QSAATLNLLRAFA GGYA + +V QW L FVE+S Q +RY++LA R+DEAL FM+A
Sbjct: 181 QAYNQSAATLNLLRAFAQGGYADLHKVHQWTLGFVEKSPQGERYRDLAGRLDEALAFMAA 240

Query: 286 CGL-GTDHPLMTTTDFYTSHECLLLPYEQSLTRLDSTSGLYYDCSAHMVWCGERTRQLDG 344
           CG+ G   P +  T+F+TSHE LLLPYEQ+LTR+DST+G +Y  SAHM+W G+RTRQ DG
Sbjct: 241 CGITGATTPQIRETEFFTSHEALLLPYEQALTRIDSTTGDWYAVSAHMLWVGDRTRQPDG 300

Query: 345 AHVEFLRGIANPLGIKVSNKMDPFELVKLVEILNPNNKPGRITVIVRMGAENMRVKLPHL 404
           AH+E+LRGI NPLG+K    +DP EL++L+++LNP ++PGR+T+I RMG + +  KLP L
Sbjct: 301 AHIEYLRGIRNPLGLKCGPSLDPDELIRLIDLLNPADEPGRLTLICRMGHDKVEDKLPAL 360

Query: 405 IRAVRRSGQIVTWVCDPMHGNTIKAPCGLKTRAFDSILAEVRAFLDVHEQEGSHAGGIHL 464
           +R V+R G+ V W CDPMHGNTIK+  G KTR FD +LAEVR F +V   E  H GG+H 
Sbjct: 361 VRKVKREGRTVVWSCDPMHGNTIKSSTGFKTRPFDRVLAEVRGFFEVCRTEDVHPGGVHF 420

Query: 465 EMTGQNVTECIGGSRTVTYDDLSSRYHTHCDPRLNASQSLELAFIVAERLRKRRTG 520
           EMTGQ+VTEC GG++ +T   L+ RYHT CDPRLNASQSLELAF+VAE L++ R G
Sbjct: 421 EMTGQDVTECTGGAQAITEHSLALRYHTACDPRLNASQSLELAFLVAEELKRTRRG 476


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: 709
Number of extensions: 22
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: 486
Length adjustment: 34
Effective length of query: 491
Effective length of database: 452
Effective search space:   221932
Effective search space used:   221932
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_012566168.1 RC1_RS04520 (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.26866.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-226  737.5   0.0   2.4e-226  737.3   0.0    1.0  1  lcl|NCBI__GCF_000016185.1:WP_012566168.1  RC1_RS04520 3-deoxy-7-phosphohep


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016185.1:WP_012566168.1  RC1_RS04520 3-deoxy-7-phosphoheptulonate synthase class II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  737.3   0.0  2.4e-226  2.4e-226       1     442 [.      30     473 ..      30     474 .. 0.99

  Alignments for each domain:
  == domain 1  score: 737.3 bits;  conditional E-value: 2.4e-226
                                 TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 
                                               w++eswr+kpa+q+P+yPd ++l+a  + l+ +PPlv+age+++lke l+++++G+afllqgGdcaesf
  lcl|NCBI__GCF_000016185.1:WP_012566168.1  30 WTPESWRAKPAMQMPTYPDPAKLQAAAARLAGYPPLVFAGEARSLKECLGRATQGQAFLLQGGDCAESF 98 
                                               89******************************************************************* PP

                                 TIGR01358  70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138
                                               +e++ +nird++rvllqma+vlt+g+  Pvvkvgr+aGq+akPrs+++e+ dgv+lp+yrGd+ing++f
  lcl|NCBI__GCF_000016185.1:WP_012566168.1  99 SEFHPNNIRDTFRVLLQMAIVLTFGGATPVVKVGRMAGQFAKPRSADMEVVDGVELPAYRGDIINGFDF 167
                                               ********************************************************************* PP

                                 TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207
                                               + +arvpdp+r+v+ay++saatlnllra+++gGyadl+kvh+W+l fv+ksp+g+ry++la ++deal 
  lcl|NCBI__GCF_000016185.1:WP_012566168.1 168 TPEARVPDPDRMVQAYNQSAATLNLLRAFAQGGYADLHKVHQWTLGFVEKSPQGERYRDLAGRLDEALA 236
                                               ********************************************************************* PP

                                 TIGR01358 208 fmsavgvaeae..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahvef 274
                                               fm a+g++ a+  +++++e++tshealll+ye+altr ds++g+++ +sah+lW+G+rtrq dgah+e+
  lcl|NCBI__GCF_000016185.1:WP_012566168.1 237 FMAACGITGATtpQIRETEFFTSHEALLLPYEQALTRIDSTTGDWYAVSAHMLWVGDRTRQPDGAHIEY 305
                                               *******9998889******************************************************* PP

                                 TIGR01358 275 lrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWv 343
                                               lrg++nP+g+k+gps+ +del++li+ l+P +ePGrltli r+G +k+ +klP l+++vk++Gr+vvW 
  lcl|NCBI__GCF_000016185.1:WP_012566168.1 306 LRGIRNPLGLKCGPSLDPDELIRLIDLLNPADEPGRLTLICRMGHDKVEDKLPALVRKVKREGRTVVWS 374
                                               ********************************************************************* PP

                                 TIGR01358 344 tdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdla 412
                                               +dpmhGnt+++++G+ktr fd++l+ev++ffev ++e +hpGGvh e+tG+dvtec+GGa++ite+ la
  lcl|NCBI__GCF_000016185.1:WP_012566168.1 375 CDPMHGNTIKSSTGFKTRPFDRVLAEVRGFFEVCRTEDVHPGGVHFEMTGQDVTECTGGAQAITEHSLA 443
                                               ********************************************************************* PP

                                 TIGR01358 413 sryetacdPrlnaeqslelaflvaeklrea 442
                                                ry+tacdPrlna+qslelaflvae l+ +
  lcl|NCBI__GCF_000016185.1:WP_012566168.1 444 LRYHTACDPRLNASQSLELAFLVAEELKRT 473
                                               **************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (486 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: 00:00:00.02
# Mc/sec: 9.19
//
[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