Alignments for a candidate for aroC in Rhodospirillum rubrum ATCC 11170

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Rhodospirillum rubrum ATCC 11170

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_011390373.1 RRU_RS13555 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>NCBI__GCF_000013085.1:WP_011390373.1
          Length = 366

 Score =  450 bits (1157), Expect = e-131
 Identities = 227/359 (63%), Positives = 278/359 (77%), Gaps = 9/359 (2%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           MAG++ G LFR T+FGESHG A+GC+V+GVPPGIPLT ADLQHDLDRR+PG SR+TTQRR
Sbjct: 1   MAGDSFGTLFRFTSFGESHGPAIGCVVEGVPPGIPLTAADLQHDLDRRKPGQSRFTTQRR 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           E D  +ILSGV+EGVTTGT I +LI NTDQRS+DYS I   FRPGHADYTY  KYG+RD 
Sbjct: 61  EDDAAEILSGVYEGVTTGTPIAVLIRNTDQRSKDYSDIAQRFRPGHADYTYWVKYGVRDP 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFG--IEIRGCLTQMGDIPLDIK--DWSQVEQN 176
           RGGGRSSARETA+RVAAGAIA+K L    G  + IR  + +MG + ++    DW  V+ N
Sbjct: 121 RGGGRSSARETAVRVAAGAIARKVLTSVLGRPLTIRAAVVEMGGLAIERANWDWLSVDAN 180

Query: 177 PFFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMS 236
           PFF PD   +   + L+  ++++G S+GA V VVA GVP GLGEPV+DRLDAD+A ALMS
Sbjct: 181 PFFSPDAAMVAPWEALLDGVRRDGSSVGAVVEVVAEGVPPGLGEPVYDRLDADLAKALMS 240

Query: 237 INAVKGVEIGDGFDVVALRGSQNRDEITKDG-----FQSNHAGGILGGISSGQQIIAHMA 291
           INAVKGVEIG GF+   LRG  N DE+  +G     F SN+AGG+LGGIS+GQ IIA +A
Sbjct: 241 INAVKGVEIGAGFEAARLRGESNADEMLPNGLGGVRFTSNNAGGVLGGISTGQTIIARLA 300

Query: 292 LKPTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQ 350
           +KPTSSI +P ++++  G  V+++TKGRHDPCVGIRAVP+AEAM+A+VL DHLLR R Q
Sbjct: 301 VKPTSSIMIPRQSVDTQGRPVDVVTKGRHDPCVGIRAVPVAEAMVAVVLADHLLRFRGQ 359


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: 443
Number of extensions: 18
Number of successful extensions: 5
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: 366
Length adjustment: 29
Effective length of query: 332
Effective length of database: 337
Effective search space:   111884
Effective search space used:   111884
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 WP_011390373.1 RRU_RS13555 (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.4191465.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.4e-138  445.4   0.0     8e-138  445.1   0.0    1.0  1  NCBI__GCF_000013085.1:WP_011390373.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000013085.1:WP_011390373.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  445.1   0.0    8e-138    8e-138       1     347 [.      10     356 ..      10     359 .. 0.98

  Alignments for each domain:
  == domain 1  score: 445.1 bits;  conditional E-value: 8e-138
                             TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaPia 73 
                                           +r+t fGeSHg+a+g++++G+P+g++lt++d+q++l+rR+pgqsr+t++r+E+D+ eilsGv+eG TtG+Pia
  NCBI__GCF_000013085.1:WP_011390373.1  10 FRFTSFGESHGPAIGCVVEGVPPGIPLTAADLQHDLDRRKPGQSRFTTQRREDDAAEILSGVYEGVTTGTPIA 82 
                                           89*********************************************************************** PP

                             TIGR00033  74 llikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketag..iei 144
                                           +li+N+d+rskdy+di++++RPgHadyty++KYg++d +gggrsSaReTa+rvaaGa+a+k L +  g  + i
  NCBI__GCF_000013085.1:WP_011390373.1  83 VLIRNTDQRSKDYSDIAQRFRPGHADYTYWVKYGVRDPRGGGRSSARETAVRVAAGAIARKVLTSVLGrpLTI 155
                                           *****************************************************************98755899 PP

                             TIGR00033 145 vayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvglGep 217
                                            a vv++g +++e+ + +     ++d++p++ pda   +  e+++d +++dg svG+vvevv+++vp glGep
  NCBI__GCF_000013085.1:WP_011390373.1 156 RAAVVEMGGLAIERANWDW---LSVDANPFFSPDAAMVAPWEALLDGVRRDGSSVGAVVEVVAEGVPPGLGEP 225
                                           *************988884...6899*********************************************** PP

                             TIGR00033 218 lfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktnnsGGieGGitnGedirvr 289
                                           ++d+lda la+al+sinAvKgveiG+GFeaa+ rG +  De+  +  +++r+ +nn GG++GGi++G+ i  r
  NCBI__GCF_000013085.1:WP_011390373.1 226 VYDRLDADLAKALMSINAVKGVEIGAGFEAARLRGESNADEMLPNgLGGVRFTSNNAGGVLGGISTGQTIIAR 298
                                           ********************************************999************************** PP

                             TIGR00033 290 iavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladallek 347
                                            avKp+++i  p+++vd+++++   +tkgRhDpcv +ravpv+Eamva+vlad+ll+ 
  NCBI__GCF_000013085.1:WP_011390373.1 299 LAVKPTSSIMIPRQSVDTQGRPVDVVTKGRHDPCVGIRAVPVAEAMVAVVLADHLLRF 356
                                           *******************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (366 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.88
//
[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