Alignments for a candidate for aroC in Xanthobacter autotrophicus Py2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Xanthobacter autotrophicus Py2

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_012116106.1 XAUT_RS20925 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>NCBI__GCF_000017645.1:WP_012116106.1
          Length = 370

 Score =  431 bits (1108), Expect = e-125
 Identities = 218/362 (60%), Positives = 267/362 (73%), Gaps = 15/362 (4%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+ NT G LFRVTTFGESHG A+GC+VDG PP +  T  D+Q  LDRRRPG SR+TTQRR
Sbjct: 1   MSFNTFGHLFRVTTFGESHGAAIGCVVDGCPPNLRFTLEDVQAALDRRRPGQSRFTTQRR 60

Query: 61  EPDQVKILSGVFEG-----VTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKY 115
           EPDQVK+LSG  E      VTTGT I LLIEN DQRS+DY+ I   +RPGHAD+TY+ KY
Sbjct: 61  EPDQVKVLSGTLEHPEGGLVTTGTPIALLIENVDQRSKDYADIAGAYRPGHADFTYDIKY 120

Query: 116 GLRDYRGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIK--DWSQV 173
           G+RD+RGGGRSSARETA RVAAGAIA K L    G+ +RG + ++G+I +D    DW++V
Sbjct: 121 GIRDHRGGGRSSARETATRVAAGAIAAKVLP---GVTVRGAVVRIGEIEIDRSRWDWNEV 177

Query: 174 EQNPFFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHA 233
             NPFFCPDP  +   +E + A++K G SIGA V +VA GVPAGLG P++ +LDAD+A A
Sbjct: 178 PNNPFFCPDPKTVPLWEEYLDAVRKAGSSIGAVVELVAEGVPAGLGAPLYGKLDADLASA 237

Query: 234 LMSINAVKGVEIGDGFDVVALRGSQNRDEIT-----KDGFQSNHAGGILGGISSGQQIIA 288
           L+ INA KGVEIG+GF+   L G +N DE+      +  F SNHAGGILGGI++G  I+A
Sbjct: 238 LLGINAAKGVEIGEGFNAAQLTGEENADEMRLGNEGRPQFLSNHAGGILGGIATGAPIVA 297

Query: 289 HMALKPTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQR 348
             ALKPTSSI  P +T++R G+E E+ TKGRHDPCVGIRAVP+ EAM+  VL DH LR R
Sbjct: 298 RFALKPTSSILTPRQTVDRTGQETEIFTKGRHDPCVGIRAVPVGEAMMWCVLADHFLRHR 357

Query: 349 AQ 350
            Q
Sbjct: 358 GQ 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: 459
Number of extensions: 16
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: 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_012116106.1 XAUT_RS20925 (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.32070.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.6e-132  426.2   0.0   5.2e-132  426.0   0.0    1.0  1  lcl|NCBI__GCF_000017645.1:WP_012116106.1  XAUT_RS20925 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017645.1:WP_012116106.1  XAUT_RS20925 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.0   0.0  5.2e-132  5.2e-132       1     349 [.      10     358 ..      10     360 .. 0.97

  Alignments for each domain:
  == domain 1  score: 426.0 bits;  conditional E-value: 5.2e-132
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfe...G. 65 
                                               +r+ttfGeSHg+a+g+++dG+P++l+ t ed+q +l+rRrpgqsr+t++r+E D+v++lsG+ e   G 
  lcl|NCBI__GCF_000017645.1:WP_012116106.1  10 FRVTTFGESHGAAIGCVVDGCPPNLRFTLEDVQAALDRRRPGQSRFTTQRREPDQVKVLSGTLEhpeGg 78 
                                               89***********************************************************97534434 PP

                                 TIGR00033  66 .kTtGaPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavak 133
                                                 TtG+Pialli+N d+rskdy di+  +RPgHad+ty  KYgi+d++gggrsSaReTa+rvaaGa+a 
  lcl|NCBI__GCF_000017645.1:WP_012116106.1  79 lVTTGTPIALLIENVDQRSKDYADIAGAYRPGHADFTYDIKYGIRDHRGGGRSSARETATRVAAGAIAA 147
                                               56******************************************************************* PP

                                 TIGR00033 134 klLketagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgv 202
                                               k L     + + + vv++ge+e++++  +    +++ ++p++cpd+++    ee++d ++k+g s+G+v
  lcl|NCBI__GCF_000017645.1:WP_012116106.1 148 KVLPG---VTVRGAVVRIGEIEIDRSRWDW---NEVPNNPFFCPDPKTVPLWEEYLDAVRKAGSSIGAV 210
                                               ***87...89**************988884...78999******************************* PP

                                 TIGR00033 203 vevvvsnvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrkt 270
                                               ve+v+++vp+glG pl+ klda lasall+inA+KgveiG+GF+aa+ +G e  De+ l  +++ ++ +
  lcl|NCBI__GCF_000017645.1:WP_012116106.1 211 VELVAEGVPAGLGAPLYGKLDADLASALLGINAAKGVEIGEGFNAAQLTGEENADEMRLGnEGRPQFLS 279
                                               **********************************************************9979999**** PP

                                 TIGR00033 271 nnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalv 339
                                               n+ GGi+GGi++G +i+ r a+Kp+++i +p++tvd +++e+   tkgRhDpcv +ravpv Eam++ v
  lcl|NCBI__GCF_000017645.1:WP_012116106.1 280 NHAGGILGGIATGAPIVARFALKPTSSILTPRQTVDRTGQETEIFTKGRHDPCVGIRAVPVGEAMMWCV 348
                                               ********************************************************************* PP

                                 TIGR00033 340 ladallekra 349
                                               lad++l++r+
  lcl|NCBI__GCF_000017645.1:WP_012116106.1 349 LADHFLRHRG 358
                                               *******987 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: 7.81
//
[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