Alignments for a candidate for aroC in Thioalkalivibrio thiocyanodenitrificans ARhD 1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Thioalkalivibrio thiocyanodenitrificans ARhD 1

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_026185919.1 THITHI_RS0100325 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>NCBI__GCF_000378965.1:WP_026185919.1
          Length = 370

 Score =  518 bits (1335), Expect = e-152
 Identities = 255/359 (71%), Positives = 298/359 (83%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+GNT G+LF VT+FGESHG A+GCIVDG PPG+ L EADLQ DL+RRRPG SR+TTQRR
Sbjct: 1   MSGNTTGKLFTVTSFGESHGPAIGCIVDGCPPGMALCEADLQPDLERRRPGKSRHTTQRR 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           E DQV+ILSGVFEGVTTGT I L+I+N DQRS+DY  I D FRPGHADYTY +KYGLRDY
Sbjct: 61  ETDQVRILSGVFEGVTTGTPIALIIDNVDQRSKDYGKIADRFRPGHADYTYFKKYGLRDY 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180
           RGGGRSSARETAMRVAAGAIAKKYL E++G+EIRG L Q+G I ++  DW  VE N FFC
Sbjct: 121 RGGGRSSARETAMRVAAGAIAKKYLRERYGVEIRGYLAQLGPIVIERLDWDAVETNAFFC 180

Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240
           PD DK+  L+  M AL+KEG+S+GA++ VVA+GVP G GEP+F+RLDADIAHA+M+INAV
Sbjct: 181 PDADKVAELEAYMDALRKEGNSVGARINVVATGVPPGWGEPIFNRLDADIAHAMMAINAV 240

Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300
           KGVEIGDGF  VA +G+++RDEIT +GF SNHAGG LGGISSGQ I   +ALKPTSSI +
Sbjct: 241 KGVEIGDGFASVAQKGTEHRDEITPEGFLSNHAGGTLGGISSGQDIRVSIALKPTSSIRL 300

Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIP 359
           PGRT++  GE  E++T GRHDPCVGIRA PIAEA LA VLMDH LR RAQ  DV T++P
Sbjct: 301 PGRTVDIRGEPAEVVTTGRHDPCVGIRATPIAEAALATVLMDHALRHRAQCGDVSTEMP 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: 491
Number of extensions: 11
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: 361
Length of database: 370
Length adjustment: 30
Effective length of query: 331
Effective length of database: 340
Effective search space:   112540
Effective search space used:   112540
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_026185919.1 THITHI_RS0100325 (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.8150.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-143  463.4   0.0   2.6e-143  463.1   0.0    1.0  1  lcl|NCBI__GCF_000378965.1:WP_026185919.1  THITHI_RS0100325 chorismate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000378965.1:WP_026185919.1  THITHI_RS0100325 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  463.1   0.0  2.6e-143  2.6e-143       1     350 [.      10     350 ..      10     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: 463.1 bits;  conditional E-value: 2.6e-143
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 
                                               +++t fGeSHg+a+g+i+dG+P+g+ l e+d+q++l+rRrpg+sr+t++r+E+D+v+ilsGvfeG TtG
  lcl|NCBI__GCF_000378965.1:WP_026185919.1  10 FTVTSFGESHGPAIGCIVDGCPPGMALCEADLQPDLERRRPGKSRHTTQRRETDQVRILSGVFEGVTTG 78 
                                               789****************************************************************** PP

                                 TIGR00033  70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138
                                               +Pial+i+N d+rskdy +i++++RPgHadyty+kKYg++d++gggrsSaReTa+rvaaGa+akk+L+e
  lcl|NCBI__GCF_000378965.1:WP_026185919.1  79 TPIALIIDNVDQRSKDYGKIADRFRPGHADYTYFKKYGLRDYRGGGRSSARETAMRVAAGAIAKKYLRE 147
                                               ********************************************************************* PP

                                 TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207
                                                +g+ei +y+ +lg + +e+        ++++++ ++cpda++ +e+e+++d ++k+g+svG++++vv+
  lcl|NCBI__GCF_000378965.1:WP_026185919.1 148 RYGVEIRGYLAQLGPIVIERLDW-----DAVETNAFFCPDADKVAELEAYMDALRKEGNSVGARINVVA 211
                                               ******************97444.....57999************************************ PP

                                 TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276
                                               ++vp g+Gep+f++lda +a+a+++inAvKgveiGdGF+++ ++G e+ De++ e     + +n+ GG+
  lcl|NCBI__GCF_000378965.1:WP_026185919.1 212 TGVPPGWGEPIFNRLDADIAHAMMAINAVKGVEIGDGFASVAQKGTEHRDEITPE----GFLSNHAGGT 276
                                               **************************************************88655....69******** PP

                                 TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladall 345
                                               +GGi+ G+dirv+ia+Kp+++i+ p +tvd++++++  +t+gRhDpcv +ra+p++Ea++a+vl+d++l
  lcl|NCBI__GCF_000378965.1:WP_026185919.1 277 LGGISSGQDIRVSIALKPTSSIRLPGRTVDIRGEPAEVVTTGRHDPCVGIRATPIAEAALATVLMDHAL 345
                                               ********************************************************************* PP

                                 TIGR00033 346 ekras 350
                                               ++ra+
  lcl|NCBI__GCF_000378965.1:WP_026185919.1 346 RHRAQ 350
                                               *9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (370 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: 10.16
//
[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