Alignments for a candidate for aroC in Sulfurimonas denitrificans DSM 1251

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Sulfurimonas denitrificans DSM 1251

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_011373637.1 SUDEN_RS10500 chorismate synthase

Query= SwissProt::P56122
         (365 letters)



>NCBI__GCF_000012965.1:WP_011373637.1
          Length = 358

 Score =  419 bits (1078), Expect = e-122
 Identities = 206/364 (56%), Positives = 275/364 (75%), Gaps = 6/364 (1%)

Query: 1   MNTLGRFLRLTTFGESHGDVIGGVLDGMPSGIKIDYALLENEMKRRQGGRNVFITPRKED 60
           MN+ G   +++TFGESHG  IG +LDG+P+G+ ID   ++ E+ RR+ G++ F T RKED
Sbjct: 1   MNSFGIKFKISTFGESHGVAIGCLLDGVPAGLLIDEEFIQAELDRRKPGKSEFETARKED 60

Query: 61  DKVEITSGVFEDFSTGTPIGFLIHNQRARSKDYDNIKNLFRPSHADFTYFHKYGIRDFRG 120
           DKVEI SGVFE  STGTPI  +I+N   +SKDY NIK++FRP HADFTYFHKYG+RD+RG
Sbjct: 61  DKVEILSGVFEGKSTGTPIAMIIYNTNQKSKDYSNIKDIFRPGHADFTYFHKYGLRDYRG 120

Query: 121 GGRSSARESAIRVAAGAFAKMLLREIGIVCESGIIEIGGIKAKNYDFNHALKSEIFALDE 180
           GGRSSARE+A RVA GA AK++L+E+GI  +SGI E+ GIK+  +D+  A KS I+ALD 
Sbjct: 121 GGRSSARETAARVAGGAVAKLMLKELGIEVQSGICEVDGIKSLEFDYESAKKSIIYALDS 180

Query: 181 EQEEAQKTAIQNAIKNHDSIGGVALIRARSIKTNQKLPIGLGQGLYAKLDAKIAEAMMGL 240
            +EEAQK AI  A   HDS+GGV+ +  + +      P+GLGQ LY K+DA +A+AMMG+
Sbjct: 181 TKEEAQKEAILRAKNEHDSVGGVSRVLIKGV------PVGLGQPLYYKMDAVLADAMMGI 234

Query: 241 NGVKAVEIGKGVESSLLKGSEYNDLMDQKGFLSNRSGGVLGGMSNGEEIIVRVHFKPTPS 300
           N VKAVEIG G+ S+ LKGS  ND +   GF++N SGG+LGG+SNGE+I++ V+FKPTPS
Sbjct: 235 NAVKAVEIGDGILSASLKGSINNDAIRADGFVTNHSGGILGGISNGEDIVMNVYFKPTPS 294

Query: 301 IFQPQRTIDINGNECECLLKGRHDPCIAIRGSVVCESLLALVLADMVLLNLTSKIEYLKT 360
           IF+ Q+TI     E +  LKGRHDPC+AIRG++VCE++ ALV+ADM+LLN+ S++  + T
Sbjct: 295 IFKEQQTITCRDEEVDFSLKGRHDPCVAIRGTIVCEAMAALVIADMLLLNMGSEMSGVLT 354

Query: 361 IYNE 364
            Y +
Sbjct: 355 YYKK 358


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: 452
Number of extensions: 17
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_011373637.1 SUDEN_RS10500 (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.4051136.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-130  420.9   0.7     2e-130  420.7   0.7    1.0  1  NCBI__GCF_000012965.1:WP_011373637.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000012965.1:WP_011373637.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.7   0.7    2e-130    2e-130       1     348 [.       8     345 ..       8     348 .. 0.96

  Alignments for each domain:
  == domain 1  score: 420.7 bits;  conditional E-value: 2e-130
                             TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaPia 73 
                                           +++ tfGeSHg a+g+++dG+Pagl ++ee iq el+rR+pg+s++++ rkE+D+veilsGvfeGk tG+Pia
  NCBI__GCF_000012965.1:WP_011373637.1   8 FKISTFGESHGVAIGCLLDGVPAGLLIDEEFIQAELDRRKPGKSEFETARKEDDKVEILSGVFEGKSTGTPIA 80 
                                           7899********************************************************************* PP

                             TIGR00033  74 llikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketagieiva 146
                                           ++i+N++++skdy++ik+++RPgHad+ty++KYg++d++gggrsSaReTaarva Gavak +Lke  gie+ +
  NCBI__GCF_000012965.1:WP_011373637.1  81 MIIYNTNQKSKDYSNIKDIFRPGHADFTYFHKYGLRDYRGGGRSSARETAARVAGGAVAKLMLKE-LGIEVQS 152
                                           *****************************************************************.88***** PP

                             TIGR00033 147 yvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvglGeplf 219
                                            + ++  ++  e        e+++ks + ++d ++e++ +e i +ak+++dsvGgv  v++++vpvglG+pl+
  NCBI__GCF_000012965.1:WP_011373637.1 153 GICEVDGIKSLEF-----DYESAKKSIIYALDSTKEEAQKEAILRAKNEHDSVGGVSRVLIKGVPVGLGQPLY 220
                                           9999998877653.....356788999********************************************** PP

                             TIGR00033 220 dkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGieGGitnGedirvriav 292
                                            k+da la a+++inAvK+veiGdG  +as +Gs  nD + ++     ++tn+sGGi+GGi+nGedi++++ +
  NCBI__GCF_000012965.1:WP_011373637.1 221 YKMDAVLADAMMGINAVKAVEIGDGILSASLKGSINNDAIRAD----GFVTNHSGGILGGISNGEDIVMNVYF 289
                                           **************************************88765....599*********************** PP

                             TIGR00033 293 KpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladallekr 348
                                           Kp+p+i k+++t++ + +e     kgRhDpcv++r ++v+Eam alv+ad+ll ++
  NCBI__GCF_000012965.1:WP_011373637.1 290 KPTPSIFKEQQTITCRDEEVDFSLKGRHDPCVAIRGTIVCEAMAALVIADMLLLNM 345
                                           ***************988888888***************************99765 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 24.70
//
[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 2024 update 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 original 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