Alignments for a candidate for aroC in Thermovibrio ammonificans HB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Thermovibrio ammonificans HB-1

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_013538290.1 THEAM_RS07790 chorismate synthase

Query= SwissProt::O66493
         (398 letters)



>NCBI__GCF_000185805.1:WP_013538290.1
          Length = 382

 Score =  456 bits (1174), Expect = e-133
 Identities = 242/387 (62%), Positives = 288/387 (74%), Gaps = 11/387 (2%)

Query: 6   LRFLTAGESHGKGLTAILEGIPANLPLSEEEINHELRRRQRGYGRGGRMKIEKDTAEILS 65
           LRF TAGESHGKG+ A LEG PAN P+  + IN E+ RRQ+GYGRGGRMKIEKD  E LS
Sbjct: 2   LRFYTAGESHGKGIFAYLEGFPANFPVDFDFINREMARRQKGYGRGGRMKIEKDRVEFLS 61

Query: 66  GVRFGKTLGSPIALFIRNRDWENWKEKMAIEGEPSPSVVPFTRPRPGHADLSGGIKYNQR 125
           GVR GKTLGSPI + + NRD++NW+E M  E    P     TRPRPGHADL G +KY   
Sbjct: 62  GVRLGKTLGSPILMAVWNRDYKNWEEVMRPEPGQLPPEKKVTRPRPGHADLPGVLKYGFD 121

Query: 126 DLRNILERASARETAARVAVGAVCKKFLSEFGIKIGSFVVSIGQKEV--EELKDKSYFAN 183
           D+RN+LER+SARETA RVA GA+CK  L   GI++GSFV+SIG  +V  E ++ KS+   
Sbjct: 122 DVRNVLERSSARETAGRVAAGALCKDLLRRLGIEVGSFVLSIGSAQVPMEAIEGKSF--- 178

Query: 184 PEKLLSYHEKAEDSELRIPF--PEKDEEFKTYIDEVKEKGESLGGVFEVFALNVPPGLGS 241
                   E AE+S++RIP   PE +E FK  ID  K KGESLGGVF VFA  VP GLGS
Sbjct: 179 ----KELFENAENSQVRIPVSDPEVEETFKREIDGAKAKGESLGGVFVVFATGVPVGLGS 234

Query: 242 HIQWDRRIDGRIAQAMMSIQAIKGVEIGLGFEAARRFGSQVHDEIGWSEGKGYFRHSNNL 301
           H QWD+R+DGRIAQA+MSIQAIKGVEIGLGFEAAR  GS+VHDEI +S+ +G++R +NN 
Sbjct: 235 HTQWDKRLDGRIAQAIMSIQAIKGVEIGLGFEAARLPGSKVHDEIFYSQERGFYRLTNNA 294

Query: 302 GGTEGGITNGMPIVVRVAMKPIPTLKNPLRSVDIETKEEMKAGKERTDIVAVPAASVVGE 361
           GG EGGITNG PIVV+ AMKPIPTL  PLRSVDI+TKE  +A  ER+D+ AVPAA+VVGE
Sbjct: 295 GGIEGGITNGEPIVVKAAMKPIPTLYKPLRSVDIKTKEPFEASVERSDVCAVPAAAVVGE 354

Query: 362 AMLAIVLADALLEKLGGDFMEEVKKRF 388
           AMLAIV+  ALLE+   D  EE++  F
Sbjct: 355 AMLAIVITAALLERYPADSFEELRLLF 381


Lambda     K      H
   0.317    0.137    0.394 

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: 498
Number of extensions: 27
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: 398
Length of database: 382
Length adjustment: 30
Effective length of query: 368
Effective length of database: 352
Effective search space:   129536
Effective search space used:   129536
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_013538290.1 THEAM_RS07790 (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.2695922.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.2e-125  402.3   0.0   9.4e-125  402.1   0.0    1.0  1  NCBI__GCF_000185805.1:WP_013538290.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000185805.1:WP_013538290.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.1   0.0  9.4e-125  9.4e-125       1     347 [.       2     368 ..       2     372 .. 0.94

  Alignments for each domain:
  == domain 1  score: 402.1 bits;  conditional E-value: 9.4e-125
                             TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaPia 73 
                                           lr+ t+GeSHgk + a ++G+Pa+++++ + i++e++rR++g++r+ rm+ E+D+ve+lsGv+ GkT G+Pi 
  NCBI__GCF_000185805.1:WP_013538290.1   2 LRFYTAGESHGKGIFAYLEGFPANFPVDFDFINREMARRQKGYGRGGRMKIEKDRVEFLSGVRLGKTLGSPIL 74 
                                           6899********************************************************************* PP

                             TIGR00033  74 llikNkd.......vrskdyed....ikelpRPgHadytylkKYgikd.regggrsSaReTaarvaaGavakk 134
                                           + + N+d       +r+++ +     + ++pRPgHad+ ++ KYg++d r+ ++rsSaReTa+rvaaGa+ k 
  NCBI__GCF_000185805.1:WP_013538290.1  75 MAVWNRDyknweevMRPEPGQLppekKVTRPRPGHADLPGVLKYGFDDvRNVLERSSARETAGRVAAGALCKD 147
                                           *******9888888777764334444999******************************************** PP

                             TIGR00033 135 lLketagieivayvvklgeveleeesak....eiskerldkspvrcp..daeaekemeeeidkakkdgdsvGg 201
                                           lL++  gie+ ++v ++g+ +++ e ++    ++  e++++s+vr+p  d+e e+  + eid ak +g+s+Gg
  NCBI__GCF_000185805.1:WP_013538290.1 148 LLRR-LGIEVGSFVLSIGSAQVPMEAIEgksfKELFENAENSQVRIPvsDPEVEETFKREIDGAKAKGESLGG 219
                                           ****.88************9999998888666445566666666654339*********************** PP

                             TIGR00033 202 vvevvvsnvpvglG..eplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktn 271
                                           v  v +++vpvglG   +++++ld+++a+a++si+A+KgveiG GFeaa+ +Gs+++De+ ++ + ++ r tn
  NCBI__GCF_000185805.1:WP_013538290.1 220 VFVVFATGVPVGLGshTQWDKRLDGRIAQAIMSIQAIKGVEIGLGFEAARLPGSKVHDEIFYSqERGFYRLTN 292
                                           **************9889*****************************************99887999****** PP

                             TIGR00033 272 nsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladal 344
                                           n GGieGGitnGe+i+v++a+Kpipt++kpl++vd++tke+ +a+++R+D+c+vp+a++v Eam+a+v++ al
  NCBI__GCF_000185805.1:WP_013538290.1 293 NAGGIEGGITNGEPIVVKAAMKPIPTLYKPLRSVDIKTKEPFEASVERSDVCAVPAAAVVGEAMLAIVITAAL 365
                                           ************************************************************************9 PP

                             TIGR00033 345 lek 347
                                           le+
  NCBI__GCF_000185805.1:WP_013538290.1 366 LER 368
                                           986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (382 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: 00:00:00.00
# Mc/sec: 14.15
//
[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 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