Alignments for a candidate for aroC in Nitratiruptor tergarcus DSM 16512

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Nitratiruptor tergarcus DSM 16512

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_084275155.1 B8779_RS03370 chorismate synthase

Query= SwissProt::P56122
         (365 letters)



>NCBI__GCF_900176045.1:WP_084275155.1
          Length = 358

 Score =  442 bits (1137), Expect = e-129
 Identities = 219/363 (60%), Positives = 280/363 (77%), Gaps = 6/363 (1%)

Query: 1   MNTLGRFLRLTTFGESHGDVIGGVLDGMPSGIKIDYALLENEMKRRQGGRNVFITPRKED 60
           MN+ G   R TTFGESHG  IG V+DG+P+G+KID   +++E+ RR+ G++ F T RKE 
Sbjct: 1   MNSFGIKFRFTTFGESHGKAIGCVVDGVPAGLKIDEEFIQSELDRRRPGKSKFATARKES 60

Query: 61  DKVEITSGVFEDFSTGTPIGFLIHNQRARSKDYDNIKNLFRPSHADFTYFHKYGIRDFRG 120
           DKVEI SGVFE  +TGTPI  +I N+  +S+DY NIK++FRP HADFTY++KYGIRD+RG
Sbjct: 61  DKVEILSGVFEGKATGTPIAMVIFNKDQKSRDYSNIKDIFRPGHADFTYYYKYGIRDYRG 120

Query: 121 GGRSSARESAIRVAAGAFAKMLLREIGIVCESGIIEIGGIKAKNYDFNHALKSEIFALDE 180
           GGRSSARE+A RVA GA AK+ L+E GI  E+G++E+ GIKAK  DF +A +SEIFALD 
Sbjct: 121 GGRSSARETAARVATGAVAKLFLKEFGIEVEAGVVEVAGIKAKKLDFKYARESEIFALDP 180

Query: 181 EQEEAQKTAIQNAIKNHDSIGGVALIRARSIKTNQKLPIGLGQGLYAKLDAKIAEAMMGL 240
             EE QK AI  A + HDS+GG  L+RAR +      P+GLG+ +Y KLDA +AEA+M +
Sbjct: 181 SVEEQQKEAILGAKEAHDSVGGAVLVRARGV------PVGLGEPIYYKLDAVLAEALMSI 234

Query: 241 NGVKAVEIGKGVESSLLKGSEYNDLMDQKGFLSNRSGGVLGGMSNGEEIIVRVHFKPTPS 300
           N  KAVEIG G E+S L GS+ ND +  +GF+SN +GG+LGG+SNGEE+I +V+FKPTPS
Sbjct: 235 NAAKAVEIGNGCEASRLLGSQNNDEITAEGFVSNNAGGILGGISNGEEVIAKVYFKPTPS 294

Query: 301 IFQPQRTIDINGNECECLLKGRHDPCIAIRGSVVCESLLALVLADMVLLNLTSKIEYLKT 360
           IFQ QR+IDI+GNE E  LKGRHDP +A RGSVV E+++ALVLADM+LLN TSK+E L+ 
Sbjct: 295 IFQKQRSIDIDGNEVEVELKGRHDPFVAARGSVVAEAMMALVLADMLLLNATSKLENLQK 354

Query: 361 IYN 363
           IYN
Sbjct: 355 IYN 357


Lambda     K      H
   0.319    0.139    0.395 

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: 424
Number of extensions: 16
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: 365
Length of database: 358
Length adjustment: 29
Effective length of query: 336
Effective length of database: 329
Effective search space:   110544
Effective search space used:   110544
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_084275155.1 B8779_RS03370 (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.21037.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-135  437.6   0.9   1.7e-135  437.4   0.9    1.0  1  lcl|NCBI__GCF_900176045.1:WP_084275155.1  B8779_RS03370 chorismate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900176045.1:WP_084275155.1  B8779_RS03370 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.4   0.9  1.7e-135  1.7e-135       1     348 [.       8     345 ..       8     348 .. 0.97

  Alignments for each domain:
  == domain 1  score: 437.4 bits;  conditional E-value: 1.7e-135
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 
                                               +r+ttfGeSHgka+g+++dG+Pagl+++ee iq+el+rRrpg+s++++ rkE+D+veilsGvfeGk tG
  lcl|NCBI__GCF_900176045.1:WP_084275155.1   8 FRFTTFGESHGKAIGCVVDGVPAGLKIDEEFIQSELDRRRPGKSKFATARKESDKVEILSGVFEGKATG 76 
                                               89******************************************************************* PP

                                 TIGR00033  70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138
                                               +Pia++i Nkd++s+dy++ik+++RPgHad+ty  KYgi+d++gggrsSaReTaarva+Gavak +Lke
  lcl|NCBI__GCF_900176045.1:WP_084275155.1  77 TPIAMVIFNKDQKSRDYSNIKDIFRPGHADFTYYYKYGIRDYRGGGRSSARETAARVATGAVAKLFLKE 145
                                               ********************************************************************* PP

                                 TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207
                                                 gie+ a vv+++ +++++  +k      + +s+++++d++ e++ +e i  ak+++dsvGg v v +
  lcl|NCBI__GCF_900176045.1:WP_084275155.1 146 -FGIEVEAGVVEVAGIKAKKLDFK-----YARESEIFALDPSVEEQQKEAILGAKEAHDSVGGAVLVRA 208
                                               .88**************9975554.....466799********************************** PP

                                 TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276
                                               ++vpvglGep++ klda la+al+sinA+K+veiG+G ea +  Gs+ nDe+++e     +++nn GGi
  lcl|NCBI__GCF_900176045.1:WP_084275155.1 209 RGVPVGLGEPIYYKLDAVLAEALMSINAAKAVEIGNGCEASRLLGSQNNDEITAE----GFVSNNAGGI 273
                                               **************************************************99887....699******* PP

                                 TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladall 345
                                               +GGi+nGe++  ++ +Kp+p+i ++++++d++++e     kgRhDp v+ r ++v+Eam+alvlad+ll
  lcl|NCBI__GCF_900176045.1:WP_084275155.1 274 LGGISNGEEVIAKVYFKPTPSIFQKQRSIDIDGNEVEVELKGRHDPFVAARGSVVAEAMMALVLADMLL 342
                                               **********************************999999***************************98 PP

                                 TIGR00033 346 ekr 348
                                                + 
  lcl|NCBI__GCF_900176045.1:WP_084275155.1 343 LNA 345
                                               765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (358 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.97
//
[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