Alignments for a candidate for aroC in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Sinorhizobium meliloti 1021

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate SMc00007 SMc00007 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>FitnessBrowser__Smeli:SMc00007
          Length = 365

 Score =  409 bits (1052), Expect = e-119
 Identities = 214/368 (58%), Positives = 267/368 (72%), Gaps = 16/368 (4%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+ NT G LFRVTT+GESHG ALGC+VDG PPGI  T A++Q  LD+R+PG SR+ TQRR
Sbjct: 1   MSHNTFGHLFRVTTWGESHGPALGCVVDGCPPGIRFTLAEVQAWLDKRKPGQSRFVTQRR 60

Query: 61  EPDQVKILSGVF---EG---VTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQK 114
           E D VK+LSGV    +G   ++TGT I ++IENTDQRS+DYS I   +RPGHADYTY+ K
Sbjct: 61  EDDLVKVLSGVMLDDDGETMISTGTPISMMIENTDQRSKDYSEIAKRYRPGHADYTYDAK 120

Query: 115 YGLRDYRGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIK--DWSQ 172
           YG+RDYRGGGRSSARETA RVAAGAIA+K +    G+ +RG L Q+G   +D    DW++
Sbjct: 121 YGIRDYRGGGRSSARETAARVAAGAIARKVVP---GLVVRGALVQIGKHRIDRSNWDWAE 177

Query: 173 VEQNPFFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAH 232
           V  NPFF PDP  +   +E +  ++K G SIGA V VVA GVPAG+G P++ +LD DIA 
Sbjct: 178 VNNNPFFAPDPAIVPVWEEYLDGIRKAGSSIGAVVEVVAEGVPAGIGAPIYAKLDQDIAA 237

Query: 233 ALMSINAVKGVEIGDGFDVVALRGSQNRDEIT-----KDGFQSNHAGGILGGISSGQQII 287
            LMSINAVKGVEIG+GF    + G +N DE+      +  F SN+AGGILGGI++GQ ++
Sbjct: 238 NLMSINAVKGVEIGNGFAAAEISGEENADEMRIGAQGEPVFLSNNAGGILGGIATGQPVV 297

Query: 288 AHMALKPTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQ 347
           A  A+KPTSSI    R+I+  G+EV++ TKGRHDPCVGIRAVPI EAMLA  + DH LR 
Sbjct: 298 ARFAIKPTSSILTERRSIDSDGKEVDVRTKGRHDPCVGIRAVPIGEAMLACAIADHYLRD 357

Query: 348 RAQNADVK 355
           R Q   +K
Sbjct: 358 RGQTGRLK 365


Lambda     K      H
   0.319    0.138    0.404 

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: 457
Number of extensions: 17
Number of successful extensions: 6
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: 361
Length of database: 365
Length adjustment: 29
Effective length of query: 332
Effective length of database: 336
Effective search space:   111552
Effective search space used:   111552
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate SMc00007 SMc00007 (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.21774.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   6.8e-126  405.9   0.1   7.8e-126  405.7   0.1    1.0  1  lcl|FitnessBrowser__Smeli:SMc00007  SMc00007 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc00007  SMc00007 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.7   0.1  7.8e-126  7.8e-126       1     350 [.      10     360 ..      10     361 .. 0.97

  Alignments for each domain:
  == domain 1  score: 405.7 bits;  conditional E-value: 7.8e-126
                           TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvf...eGkT...tG 69 
                                         +r+tt+GeSHg+alg+++dG+P+g++ t +++q  l++R+pgqsr+ ++r+E+D v++lsGv+    G+T   tG
  lcl|FitnessBrowser__Smeli:SMc00007  10 FRVTTWGESHGPALGCVVDGCPPGIRFTLAEVQAWLDKRKPGQSRFVTQRREDDLVKVLSGVMlddDGETmisTG 84 
                                         89************************************************************755579985557* PP

                           TIGR00033  70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketagiei 144
                                         +Pi+++i+N+d+rskdy++i++++RPgHadyty  KYgi+d++gggrsSaReTaarvaaGa+a+k +     + +
  lcl|FitnessBrowser__Smeli:SMc00007  85 TPISMMIENTDQRSKDYSEIAKRYRPGHADYTYDAKYGIRDYRGGGRSSARETAARVAAGAIARKVVPG---LVV 156
                                         *****************************************************************9987...679 PP

                           TIGR00033 145 vayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvglGeplf 219
                                          + +v++g+ ++++++ +     +++++p+++pd+      ee++d ++k+g s+G+vvevv+++vp+g+G p++
  lcl|FitnessBrowser__Smeli:SMc00007 157 RGALVQIGKHRIDRSNWDW---AEVNNNPFFAPDPAIVPVWEEYLDGIRKAGSSIGAVVEVVAEGVPAGIGAPIY 228
                                         9************998884...68999************************************************ PP

                           TIGR00033 220 dkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktnnsGGieGGitnGedirvriavK 293
                                          kld  +a+ l+sinAvKgveiG+GF+aa++ G e  De+ +  +++  + +nn GGi+GGi++G++++ r a+K
  lcl|FitnessBrowser__Smeli:SMc00007 229 AKLDQDIAANLMSINAVKGVEIGNGFAAAEISGEENADEMRIGaQGEPVFLSNNAGGILGGIATGQPVVARFAIK 303
                                         *****************************************998999**************************** PP

                           TIGR00033 294 piptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladallekras 350
                                         p+++i ++++++d ++ke   +tkgRhDpcv +ravp+ Eam+a  +ad++l++r++
  lcl|FitnessBrowser__Smeli:SMc00007 304 PTSSILTERRSIDSDGKEVDVRTKGRHDPCVGIRAVPIGEAMLACAIADHYLRDRGQ 360
                                         ****************************************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (365 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: 10.33
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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