Alignments for a candidate for aroC in Thermomonospora curvata DSM 43183

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Thermomonospora curvata DSM 43183

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_012853279.1 TCUR_RS14560 chorismate synthase

Query= SwissProt::P9WPY1
         (401 letters)



>NCBI__GCF_000024385.1:WP_012853279.1
          Length = 392

 Score =  557 bits (1435), Expect = e-163
 Identities = 285/389 (73%), Positives = 318/389 (81%)

Query: 1   MLRWITAGESHGRALVAVVEGMVAGVHVTSADIADQLARRRLGYGRGARMTFERDAVTVL 60
           MLRW+TAGESHG ALVA+VEG+ AGV VTS DIA++L RRRLG+GRGARM FE+D VT+ 
Sbjct: 1   MLRWLTAGESHGPALVAIVEGLPAGVQVTSGDIAEELRRRRLGHGRGARMKFEQDEVTIT 60

Query: 61  SGIRHGSTLGGPIAIEIGNTEWPKWETVMAADPVDPAELADVARNAPLTRPRPGHADYAG 120
            GIRHG TLGGP+AIE+GNTEWPKWETVMAADPVDP  LA  ARNAPLTRPRPGHAD  G
Sbjct: 61  GGIRHGRTLGGPVAIEVGNTEWPKWETVMAADPVDPQVLAGQARNAPLTRPRPGHADLVG 120

Query: 121 MLKYGFDDARPVLERASARETAARVAAGTVARAFLRQALGVEVLSHVISIGASAPYEGPP 180
           M KYGFDDARPVLERASARETAARVA G VA+AFLRQALGVEVLSHV+++G     EG  
Sbjct: 121 MQKYGFDDARPVLERASARETAARVALGAVAKAFLRQALGVEVLSHVVALGEVTAPEGLQ 180

Query: 181 PRAEDLPAIDASPVRAYDKAAEADMIAQIEAAKKDGDTLGGVVEAVALGLPVGLGSFTSG 240
           P   DLPAIDA PVR +D    A+M+A I+A +K GDT+GGVVE +A GLP GLGS    
Sbjct: 181 PTPADLPAIDADPVRCFDAETSAEMVAHIDALRKAGDTIGGVVEVLAYGLPPGLGSHVHW 240

Query: 241 DHRLDSQLAAAVMGIQAIKGVEIGDGFQTARRRGSRAHDEMYPGPDGVVRSTNRAGGLEG 300
           D RLD++LA A+MGIQAIKGVEIGDGF TARR GSRAHDE+  GPDG+ R TNRAGG+EG
Sbjct: 241 DRRLDARLAGALMGIQAIKGVEIGDGFATARRPGSRAHDEIEDGPDGLRRRTNRAGGVEG 300

Query: 301 GMTNGQPLRVRAAMKPISTVPRALATVDLATGDEAVAIHQRSDVCAVPAAGVVVETMVAL 360
           GMT G+ LRVRAAMKPISTVPRAL TVD+ T + A AI+QRSDV AVPAAGVV E MVAL
Sbjct: 301 GMTTGEVLRVRAAMKPISTVPRALDTVDVTTREPAKAINQRSDVTAVPAAGVVAEAMVAL 360

Query: 361 VLARAALEKFGGDSLAETQRNIAAYQRSV 389
           VLA AALEKFGGDS+ ET RN   Y  S+
Sbjct: 361 VLADAALEKFGGDSVEETARNAQGYLSSL 389


Lambda     K      H
   0.317    0.133    0.380 

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: 574
Number of extensions: 22
Number of successful extensions: 1
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: 401
Length of database: 392
Length adjustment: 31
Effective length of query: 370
Effective length of database: 361
Effective search space:   133570
Effective search space used:   133570
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: 50 (23.9 bits)

Align candidate WP_012853279.1 TCUR_RS14560 (chorismate synthase)
to HMM TIGR00033 (aroC: chorismate synthase (EC 4.2.3.5))

# 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/TIGR00033.hmm
# target sequence database:        /tmp/gapView.17903.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00033  [M=351]
Accession:   TIGR00033
Description: aroC: chorismate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-136  441.5   0.1   1.2e-136  441.3   0.1    1.0  1  lcl|NCBI__GCF_000024385.1:WP_012853279.1  TCUR_RS14560 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024385.1:WP_012853279.1  TCUR_RS14560 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.3   0.1  1.2e-136  1.2e-136       1     350 [.       2     372 ..       2     373 .. 0.97

  Alignments for each domain:
  == domain 1  score: 441.3 bits;  conditional E-value: 1.2e-136
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 
                                               lr++t+GeSHg+al+ai++GlPag+++t  di++el+rRr g++r++rm+ E+Dev+i++G+++G+T G
  lcl|NCBI__GCF_000024385.1:WP_012853279.1   2 LRWLTAGESHGPALVAIVEGLPAGVQVTSGDIAEELRRRRLGHGRGARMKFEQDEVTITGGIRHGRTLG 70 
                                               69******************************************************************* PP

                                 TIGR00033  70 aPiallikNkd.......vrskdyed..........ikelpRPgHadytylkKYgikd.regggrsSaR 120
                                                P+a+ + N++       +++++++             ++pRPgHad+++++KYg++d r  ++r+SaR
  lcl|NCBI__GCF_000024385.1:WP_012853279.1  71 GPVAIEVGNTEwpkwetvMAADPVDPqvlagqarnaPLTRPRPGHADLVGMQKYGFDDaRPVLERASAR 139
                                               ******************99999999999999999999********************99********* PP

                                 TIGR00033 121 eTaarvaaGavakklLketagieivayvvklgeveleeesak.eiskerldkspvrcpdaeaekemeee 188
                                               eTaarva Gavak++L++  g+e++++vv lgev+++e          ++d++pvrc dae+++em++ 
  lcl|NCBI__GCF_000024385.1:WP_012853279.1 140 ETAARVALGAVAKAFLRQALGVEVLSHVVALGEVTAPEGLQPtPADLPAIDADPVRCFDAETSAEMVAH 208
                                               **********************************999865554456789999***************** PP

                                 TIGR00033 189 idkakkdgdsvGgvvevvvsnvpvglG..eplfdkldaelasallsinAvKgveiGdGFeaasvrGsea 255
                                               id ++k+gd++Ggvvev+++++p glG  ++++++lda+la al++i+A+KgveiGdGF++a+++Gs+a
  lcl|NCBI__GCF_000024385.1:WP_012853279.1 209 IDALRKAGDTIGGVVEVLAYGLPPGLGshVHWDRRLDARLAGALMGIQAIKGVEIGDGFATARRPGSRA 277
                                               ***************************9999************************************** PP

                                 TIGR00033 256 nDelvleddkirrktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcv 324
                                               +De++   d++rr+tn+ GG+eGG+t+Ge +rvr+a+Kpi+t+ ++l tvd++t+e+aka ++R+D+++
  lcl|NCBI__GCF_000024385.1:WP_012853279.1 278 HDEIEDGPDGLRRRTNRAGGVEGGMTTGEVLRVRAAMKPISTVPRALDTVDVTTREPAKAINQRSDVTA 346
                                               ********************************************************************* PP

                                 TIGR00033 325 vpravpvvEamvalvladallekras 350
                                               vp+a++v+Eamvalvlada+lek++ 
  lcl|NCBI__GCF_000024385.1:WP_012853279.1 347 VPAAGVVAEAMVALVLADAALEKFGG 372
                                               **********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (392 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: 12.38
//
[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