Alignments for a candidate for aroA in Nocardiopsis lucentensis DSM 44048

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Nocardiopsis lucentensis DSM 44048

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_017596869.1 D471_RS0100820 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::A3TGI7
         (432 letters)



>NCBI__GCF_000341125.1:WP_017596869.1
          Length = 427

 Score =  479 bits (1234), Expect = e-140
 Identities = 245/417 (58%), Positives = 296/417 (70%), Gaps = 2/417 (0%)

Query: 6   WTCPAAEGPVAATIDLPGSKSLTNRFLVLAARAGGVSRLRSPLRSRDTLLMAQALGGLGV 65
           W  P A+ PV+A + LPGSKS+TNR LVLAA +     +R PL SRD+ LM  AL  LGV
Sbjct: 12  WHAPTAQRPVSARLSLPGSKSVTNRALVLAALSETPCVVRRPLASRDSELMIGALRALGV 71

Query: 66  GIDDVDGDDWLVTPGEVMGPADIDCGLAGTVMRFVPPLAALARGAVRFDGDPHARTRPMG 125
           G+   DG+D +VTP  + GPA +D G AGTVMRFVPPLAALA G V FDGDP AR RP+ 
Sbjct: 72  GVTQ-DGEDLVVTPAALRGPASVDVGNAGTVMRFVPPLAALADGDVHFDGDPRARERPVD 130

Query: 126 PALDALRHLGVDLDDDGRGALPFTVRGTGSVRGGDVTLDASASSQFISALLLSAPHYDQG 185
             L+ALR LG D+DD GRGALP T+ GTG+V GG+V LDAS SSQF+SALLLS   + QG
Sbjct: 131 ELLNALRALGADIDDGGRGALPMTIHGTGAVPGGEVVLDASGSSQFVSALLLSGARFAQG 190

Query: 186 VTIHHQGEPVPSQPHIDMTVEALRDAGADVDDTEADTWRVEPGPLNPLDVQIEPDLSNAA 245
           V + HQG PVPSQPH+DMTVE LR  G  V   E ++WRVEPGP+   ++ +EPDLSNAA
Sbjct: 191 VHVRHQGPPVPSQPHLDMTVEMLRAVGVSVSTGE-NSWRVEPGPVKATEITVEPDLSNAA 249

Query: 246 PFLAAALVTGGRVRISSWPQHTTQAGDEIRDILDEMGADVSLGRDGLTVSAVDGFSGVDV 305
           PFLAAALV+GG V I  WP+HTTQ GDE+R +   MG +VS     LT+      +G+  
Sbjct: 250 PFLAAALVSGGEVTIQGWPEHTTQPGDELRSLFTRMGGEVSRSGGDLTLRGTGQVNGITA 309

Query: 306 DLHDASELTPVVAALAALAQGPSLIRGVAHIRGHETDRLAALARELNALGATVTETADGL 365
           DL D  ELTP +AA+AALA  PS + G+AH+R HETDR+AALA E+N LG  V E +DGL
Sbjct: 310 DLRDVGELTPTIAAVAALADTPSRLTGIAHLRRHETDRIAALAAEINHLGGDVEELSDGL 369

Query: 366 HIVPRPLSPTMFHTYGDHRMVMAGAVIGLAVPGVVIEDVGTVAKTLPTFTDLWAHML 422
            I PRPL   +FH+Y DHRM  +GAVIGL+VPGV +E++ T  KTLP F  LWA  L
Sbjct: 370 VIRPRPLHGGVFHSYDDHRMATSGAVIGLSVPGVEVENIATTRKTLPDFPGLWAEAL 426


Lambda     K      H
   0.318    0.136    0.411 

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: 685
Number of extensions: 40
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: 432
Length of database: 427
Length adjustment: 32
Effective length of query: 400
Effective length of database: 395
Effective search space:   158000
Effective search space used:   158000
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: 51 (24.3 bits)

Align candidate WP_017596869.1 D471_RS0100820 (3-phosphoshikimate 1-carboxyvinyltransferase)
to HMM TIGR01356 (aroA: 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19))

# 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/TIGR01356.hmm
# target sequence database:        /tmp/gapView.10621.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01356  [M=415]
Accession:   TIGR01356
Description: aroA: 3-phosphoshikimate 1-carboxyvinyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-123  397.9   0.0   2.8e-123  397.7   0.0    1.0  1  lcl|NCBI__GCF_000341125.1:WP_017596869.1  D471_RS0100820 3-phosphoshikimat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000341125.1:WP_017596869.1  D471_RS0100820 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.7   0.0  2.8e-123  2.8e-123       2     411 ..      24     424 ..      23     427 .] 0.97

  Alignments for each domain:
  == domain 1  score: 397.7 bits;  conditional E-value: 2.8e-123
                                 TIGR01356   2 eikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgglkepe 70 
                                               ++++pgsKS+++Ral+laaL+e+++vv+++L s+D + ++ alr+lG+ v++++e+lv+++ +   +  
  lcl|NCBI__GCF_000341125.1:WP_017596869.1  24 RLSLPGSKSVTNRALVLAALSETPCVVRRPLASRDSELMIGALRALGVGVTQDGEDLVVTPAA--LRGP 90 
                                               5789*********************************************************77..5555 PP

                                 TIGR01356  71 aeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp 139
                                               a++d+gn+Gt++R++ +++ala+g+v+++gd++ ++RP+++l++aLr+lga+i++   +g lP++i+g+
  lcl|NCBI__GCF_000341125.1:WP_017596869.1  91 ASVDVGNAGTVMRFVPPLAALADGDVHFDGDPRARERPVDELLNALRALGADIDDGG-RGALPMTIHGT 158
                                               7*****************************************************866.79********9 PP

                                 TIGR01356 140 ..lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederk 206
                                                 ++gg v l++s SsQ++salll++++  q+v ++++g ++ s+p++++t+++l++ gv+v+  ++ +
  lcl|NCBI__GCF_000341125.1:WP_017596869.1 159 gaVPGGEVVLDASGSSQFVSALLLSGARFAQGVHVRHQGPPVPSQPHLDMTVEMLRAVGVSVSTGEN-S 226
                                               99999**********************************************************9875.* PP

                                 TIGR01356 207 ivvkggqkykqkevevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGadveveeq 275
                                               ++v++g   k +e++ve D+S+Aa flaaa+++g+evt++++ e++tq+++++ +++ +mG++v++   
  lcl|NCBI__GCF_000341125.1:WP_017596869.1 227 WRVEPGP-VKATEITVEPDLSNAAPFLAAALVSGGEVTIQGWPEHTTQPGDELRSLFTRMGGEVSRSGG 294
                                               *****97.77777******************************************************** PP

                                 TIGR01356 276 rdvevegasklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGv 344
                                                d++++g+ +++g++  +d+ ++ +++pt+a++aa+A++++r+++i++lR +E+dRiaa+a+e+++lG 
  lcl|NCBI__GCF_000341125.1:WP_017596869.1 295 -DLTLRGTGQVNGIT--ADLRDVGELTPTIAAVAALADTPSRLTGIAHLRRHETDRIAALAAEINHLGG 360
                                               .8*************..**************************************************** PP

                                 TIGR01356 345 eveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleq 411
                                               +veel+dgl+i+++   l+g+v ++ydDHR+a++ av+gl +  +ve+e+ ++++k+ P+F  ++++
  lcl|NCBI__GCF_000341125.1:WP_017596869.1 361 DVEELSDGLVIRPRP--LHGGVFHSYDDHRMATSGAVIGLSVP-GVEVENIATTRKTLPDFPGLWAE 424
                                               **************5..*************************9.*****************877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (427 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: 10.26
//
[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