Alignments for a candidate for aroC in Haloglycomyces albus DSM 45210

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Haloglycomyces albus DSM 45210

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_025274782.1 HALAL_RS0115000 chorismate synthase

Query= SwissProt::P9WPY1
         (401 letters)



>NCBI__GCF_000527155.1:WP_025274782.1
          Length = 395

 Score =  480 bits (1236), Expect = e-140
 Identities = 240/390 (61%), Positives = 296/390 (75%)

Query: 1   MLRWITAGESHGRALVAVVEGMVAGVHVTSADIADQLARRRLGYGRGARMTFERDAVTVL 60
           MLRW+TAGESHG  LV  V+G+ AG+ +T+  IA +LARRRLGYGRGARM FE D V+ +
Sbjct: 1   MLRWMTAGESHGPELVVTVDGLPAGIAITTEVIAAELARRRLGYGRGARMKFEADDVSFI 60

Query: 61  SGIRHGSTLGGPIAIEIGNTEWPKWETVMAADPVDPAELADVARNAPLTRPRPGHADYAG 120
            G+RHG TLG P+AI IGNTEWPKWE VMAADPV   EL  +ARNAPL RPRPGHAD AG
Sbjct: 61  GGVRHGYTLGSPVAIRIGNTEWPKWEKVMAADPVPEDELEGLARNAPLRRPRPGHADLAG 120

Query: 121 MLKYGFDDARPVLERASARETAARVAAGTVARAFLRQALGVEVLSHVISIGASAPYEGPP 180
           M KY   D+RP+LERASARETAARVA G + +AF++QA G++VLSH+ +IG+ +      
Sbjct: 121 MQKYSHRDSRPILERASARETAARVAGGALVKAFIKQAYGIDVLSHITTIGSVSIATDRR 180

Query: 181 PRAEDLPAIDASPVRAYDKAAEADMIAQIEAAKKDGDTLGGVVEAVALGLPVGLGSFTSG 240
           P A+DLP+IDA P+R  D  A A M+A+++AAKKD +TLGGV E +   +P GLGS    
Sbjct: 181 PSADDLPSIDADPLRTVDPDASARMVAEVDAAKKDANTLGGVAEIIGFNVPPGLGSHVQW 240

Query: 241 DHRLDSQLAAAVMGIQAIKGVEIGDGFQTARRRGSRAHDEMYPGPDGVVRSTNRAGGLEG 300
           D +LD++LAAA+M IQ++K VE+GDGF  A+  GS+AHDEM P   GV R T+RAGGLEG
Sbjct: 241 DRKLDARLAAALMSIQSVKAVEMGDGFAQAQSFGSQAHDEMVPTDTGVHRLTDRAGGLEG 300

Query: 301 GMTNGQPLRVRAAMKPISTVPRALATVDLATGDEAVAIHQRSDVCAVPAAGVVVETMVAL 360
           G+T GQPLR  AA KPIS++ R L TVD+ +G+ A AI+QRSDVCAVPA GVV E+MVA 
Sbjct: 301 GITTGQPLRASAAFKPISSLTRPLQTVDVDSGEAAEAINQRSDVCAVPAGGVVAESMVAY 360

Query: 361 VLARAALEKFGGDSLAETQRNIAAYQRSVA 390
           V+A AALEKFGGD++ ET RN A Y   +A
Sbjct: 361 VIAEAALEKFGGDNIVETSRNAAGYLNGLA 390


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: 478
Number of extensions: 17
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: 401
Length of database: 395
Length adjustment: 31
Effective length of query: 370
Effective length of database: 364
Effective search space:   134680
Effective search space used:   134680
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_025274782.1 HALAL_RS0115000 (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.24834.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.9e-126  406.3   0.1   5.7e-126  406.1   0.1    1.0  1  lcl|NCBI__GCF_000527155.1:WP_025274782.1  HALAL_RS0115000 chorismate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000527155.1:WP_025274782.1  HALAL_RS0115000 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.1   0.1  5.7e-126  5.7e-126       1     350 [.       2     372 ..       2     373 .. 0.97

  Alignments for each domain:
  == domain 1  score: 406.1 bits;  conditional E-value: 5.7e-126
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 
                                               lr++t+GeSHg++l++++dGlPag+ +t+e i+ el+rRr g++r++rm+ E+D v +++Gv++G+T G
  lcl|NCBI__GCF_000527155.1:WP_025274782.1   2 LRWMTAGESHGPELVVTVDGLPAGIAITTEVIAAELARRRLGYGRGARMKFEADDVSFIGGVRHGYTLG 70 
                                               69******************************************************************* PP

                                 TIGR00033  70 aPiallikNkd.......vrskdyed..........ikelpRPgHadytylkKYgikd.regggrsSaR 120
                                               +P+a+ i N++       ++++++ +            ++pRPgHad+++++KY  +d r +++r+SaR
  lcl|NCBI__GCF_000527155.1:WP_025274782.1  71 SPVAIRIGNTEwpkwekvMAADPVPEdeleglarnaPLRRPRPGHADLAGMQKYSHRDsRPILERASAR 139
                                               *****************9999999888999999999999*******************999******** PP

                                 TIGR00033 121 eTaarvaaGavakklLketagieivayvvklgeveleeesak.eiskerldkspvrcpdaeaekemeee 188
                                               eTaarva Ga++k+++k+ +gi ++++++++g+v++ ++         ++d++p+r +d++a+++m++e
  lcl|NCBI__GCF_000527155.1:WP_025274782.1 140 ETAARVAGGALVKAFIKQAYGIDVLSHITTIGSVSIATDRRPsADDLPSIDADPLRTVDPDASARMVAE 208
                                               *********************************9888766554446789999***************** PP

                                 TIGR00033 189 idkakkdgdsvGgvvevvvsnvpvglG..eplfdkldaelasallsinAvKgveiGdGFeaasvrGsea 255
                                               +d akkd +++Ggv e++  nvp glG  +++++klda+la+al+si+ vK+ve+GdGF++a+  Gs+a
  lcl|NCBI__GCF_000527155.1:WP_025274782.1 209 VDAAKKDANTLGGVAEIIGFNVPPGLGshVQWDRKLDARLAAALMSIQSVKAVEMGDGFAQAQSFGSQA 277
                                               ***************************9999************************************** PP

                                 TIGR00033 256 nDelvleddkirrktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcv 324
                                               +De+v +d++++r t++ GG+eGGit+G+++r ++a+Kpi+++++pl+tvd++  e+a+a ++R+D+c+
  lcl|NCBI__GCF_000527155.1:WP_025274782.1 278 HDEMVPTDTGVHRLTDRAGGLEGGITTGQPLRASAAFKPISSLTRPLQTVDVDSGEAAEAINQRSDVCA 346
                                               ********************************************************************* PP

                                 TIGR00033 325 vpravpvvEamvalvladallekras 350
                                               vp+ ++v+E+mva v+a+a+lek++ 
  lcl|NCBI__GCF_000527155.1:WP_025274782.1 347 VPAGGVVAESMVAYVIAEAALEKFGG 372
                                               **********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (395 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: 9.56
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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