Alignments for a candidate for aroC in Haloechinothrix alba DSM 45207

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Haloechinothrix alba DSM 45207

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_089301132.1 CHB84_RS09265 chorismate synthase

Query= SwissProt::P9WPY1
         (401 letters)



>NCBI__GCF_900188115.1:WP_089301132.1
          Length = 397

 Score =  529 bits (1362), Expect = e-155
 Identities = 262/393 (66%), Positives = 319/393 (81%), Gaps = 2/393 (0%)

Query: 1   MLRWITAGESHGRALVAVVEGMVAGVHVTSADIADQLARRRLGYGRGARMTFERDAVTVL 60
           MLRW+TAGESHG +L AV+EGMVAGV +T++++ +QLARRRLG+GR  RM FE DA    
Sbjct: 1   MLRWMTAGESHGPSLAAVLEGMVAGVRITTSELGEQLARRRLGFGRSPRMGFETDAAEFT 60

Query: 61  SGIRHGSTLGGPIAIEIGNTEWPKWETVMAADPVDPAELADVARNAPLTRPRPGHADYAG 120
            G+RHG T GGPI+++I N+EWPKWE VMAADPVDPAE+  +ARN PLTRPRPGHAD  G
Sbjct: 61  GGVRHGLTQGGPISVQIPNSEWPKWEKVMAADPVDPAEIDGLARNEPLTRPRPGHADLPG 120

Query: 121 MLKYGFDDARPVLERASARETAARVAAGTVARAFLRQALGVEVLSHVISIGASAPYEGPP 180
           MLKYGFD+ARPVLERASARETAAR A GTVARA+LRQ LGVE++SHV+SIG +   +GP 
Sbjct: 121 MLKYGFDEARPVLERASARETAARTALGTVARAYLRQLLGVEIISHVVSIGRAEAVDGPL 180

Query: 181 PRAEDLPAIDASPVRAYDKAAEADMIAQIEAAKKDGDTLGGVVEAVALGLPVGLGSFTSG 240
           P  +DL  +D SPVRAY +A+   M+ +++A +K GDT+GGV+E +A GLP GLGS    
Sbjct: 181 PGPDDLAGVDESPVRAYLQASTDAMVHEVDAVRKAGDTVGGVIEVIAYGLPPGLGSHVHW 240

Query: 241 DHRLDSQLAAAVMGIQAIKGVEIGDGFQTARRRGSRAHDE--MYPGPDGVVRSTNRAGGL 298
           D RLDS+LA A+MG+QA+KGVE+GDGF TA R GS+AHDE  +  G  GV R +NRAGGL
Sbjct: 241 DRRLDSRLAGALMGVQAMKGVEVGDGFTTAHRWGSQAHDEIDISDGAGGVTRRSNRAGGL 300

Query: 299 EGGMTNGQPLRVRAAMKPISTVPRALATVDLATGDEAVAIHQRSDVCAVPAAGVVVETMV 358
           EGG+TNG+PLRVR AMKPISTVPRALATVD+AT + A AIHQRSDVCAVP AGVV+E++ 
Sbjct: 301 EGGITNGEPLRVRVAMKPISTVPRALATVDVATKEAAEAIHQRSDVCAVPRAGVVLESVT 360

Query: 359 ALVLARAALEKFGGDSLAETQRNIAAYQRSVAD 391
           AL+LA AALEKFGGDSLAE++RN  AY  ++ +
Sbjct: 361 ALILAGAALEKFGGDSLAESKRNAEAYMTNLEE 393


Lambda     K      H
   0.317    0.133    0.380 

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: 538
Number of extensions: 21
Number of successful extensions: 3
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: 401
Length of database: 397
Length adjustment: 31
Effective length of query: 370
Effective length of database: 366
Effective search space:   135420
Effective search space used:   135420
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_089301132.1 CHB84_RS09265 (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.14328.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.6e-121  388.9   0.0   1.1e-120  388.7   0.0    1.0  1  lcl|NCBI__GCF_900188115.1:WP_089301132.1  CHB84_RS09265 chorismate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900188115.1:WP_089301132.1  CHB84_RS09265 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  388.7   0.0  1.1e-120  1.1e-120       1     350 [.       2     374 ..       2     375 .. 0.96

  Alignments for each domain:
  == domain 1  score: 388.7 bits;  conditional E-value: 1.1e-120
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 
                                               lr++t+GeSHg++l+a+++G+ ag+++t++++ ++l+rRr g +r  rm  E+D+ e+++Gv++G T+G
  lcl|NCBI__GCF_900188115.1:WP_089301132.1   2 LRWMTAGESHGPSLAAVLEGMVAGVRITTSELGEQLARRRLGFGRSPRMGFETDAAEFTGGVRHGLTQG 70 
                                               69******************************************************************* PP

                                 TIGR00033  70 aPiallikNkd.......vrskdyed..........ikelpRPgHadytylkKYgikd.regggrsSaR 120
                                                Pi+++i N +       +++++++             ++pRPgHad+ ++ KYg+++ r  ++r+SaR
  lcl|NCBI__GCF_900188115.1:WP_089301132.1  71 GPISVQIPNSEwpkwekvMAADPVDPaeidglarnePLTRPRPGHADLPGMLKYGFDEaRPVLERASAR 139
                                               ******************99999998999999999999********************99********* PP

                                 TIGR00033 121 eTaarvaaGavakklLketagieivayvvklgeveleeesak.eiskerldkspvrcpdaeaekemeee 188
                                               eTaar+a G+va+++L++  g+ei+++vv++g  e+ +           +d+spvr++ +  +++m++e
  lcl|NCBI__GCF_900188115.1:WP_089301132.1 140 ETAARTALGTVARAYLRQLLGVEIISHVVSIGRAEAVDGPLPgPDDLAGVDESPVRAYLQASTDAMVHE 208
                                               *********************************887766655544678999****************** PP

                                 TIGR00033 189 idkakkdgdsvGgvvevvvsnvpvglG..eplfdkldaelasallsinAvKgveiGdGFeaasvrGsea 255
                                               +d ++k+gd+vGgv+ev+++++p glG  ++++++ld++la al++++A+Kgve+GdGF++a++ Gs+a
  lcl|NCBI__GCF_900188115.1:WP_089301132.1 209 VDAVRKAGDTVGGVIEVIAYGLPPGLGshVHWDRRLDSRLAGALMGVQAMKGVEVGDGFTTAHRWGSQA 277
                                               ***************************9999************************************** PP

                                 TIGR00033 256 nDelvle..ddkirrktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDp 322
                                               +De++++   ++++r++n+ GG+eGGitnGe++rvr+a+Kpi+t+ ++l+tvd++tke+a+a ++R+D+
  lcl|NCBI__GCF_900188115.1:WP_089301132.1 278 HDEIDISdgAGGVTRRSNRAGGLEGGITNGEPLRVRVAMKPISTVPRALATVDVATKEAAEAIHQRSDV 346
                                               ******977789********************************************************* PP

                                 TIGR00033 323 cvvpravpvvEamvalvladallekras 350
                                               c+vpra++v E+++al+la a+lek++ 
  lcl|NCBI__GCF_900188115.1:WP_089301132.1 347 CAVPRAGVVLESVTALILAGAALEKFGG 374
                                               ************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (397 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: 00:00:00.01
# Mc/sec: 10.48
//
[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