Alignments for a candidate for aroA in Methanococcus aeolicus Nankai-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Methanococcus aeolicus Nankai-3

Align 3-phosphoshikimate 1-carboxyvinyltransferase; EC 2.5.1.19; 5-enolpyruvylshikimate-3-phosphate synthase; EPSP synthase; EPSPS (uncharacterized)
to candidate WP_011972873.1 MAEO_RS00750 3-phosphoshikimate 1-carboxyvinyltransferase

Query= curated2:A6UTB9
         (433 letters)



>NCBI__GCF_000017185.1:WP_011972873.1
          Length = 433

 Score =  852 bits (2200), Expect = 0.0
 Identities = 433/433 (100%), Positives = 433/433 (100%)

Query: 1   MIIIEKTEQIKGTINAPPSKSYTHRAVICASLADGTSEIISPLNSADCLSSVHGAMMLGA 60
           MIIIEKTEQIKGTINAPPSKSYTHRAVICASLADGTSEIISPLNSADCLSSVHGAMMLGA
Sbjct: 1   MIIIEKTEQIKGTINAPPSKSYTHRAVICASLADGTSEIISPLNSADCLSSVHGAMMLGA 60

Query: 61  EIDATDKNKWVVVGNNNSPKTPNNVVDIGNSGTTLRILTGIASQIPEGYAILTGDSSIIT 120
           EIDATDKNKWVVVGNNNSPKTPNNVVDIGNSGTTLRILTGIASQIPEGYAILTGDSSIIT
Sbjct: 61  EIDATDKNKWVVVGNNNSPKTPNNVVDIGNSGTTLRILTGIASQIPEGYAILTGDSSIIT 120

Query: 121 RPMQPLLDALNQLGIRAFSSKTDGTAPIIVEHGEIKNNVVKIRGDMSSQFITSLMMTMPF 180
           RPMQPLLDALNQLGIRAFSSKTDGTAPIIVEHGEIKNNVVKIRGDMSSQFITSLMMTMPF
Sbjct: 121 RPMQPLLDALNQLGIRAFSSKTDGTAPIIVEHGEIKNNVVKIRGDMSSQFITSLMMTMPF 180

Query: 181 SKMDSTIELTTPLKSAPYLDITIDVLDKFGVKIEKVKNKNKLTKFIIKGNQKYKPYSYTV 240
           SKMDSTIELTTPLKSAPYLDITIDVLDKFGVKIEKVKNKNKLTKFIIKGNQKYKPYSYTV
Sbjct: 181 SKMDSTIELTTPLKSAPYLDITIDVLDKFGVKIEKVKNKNKLTKFIIKGNQKYKPYSYTV 240

Query: 241 EGDCSSASYFIAAGVLMNSDITINNIFKNSKQGDREIVNIVKKMGAPIIEEEDKIIIKGP 300
           EGDCSSASYFIAAGVLMNSDITINNIFKNSKQGDREIVNIVKKMGAPIIEEEDKIIIKGP
Sbjct: 241 EGDCSSASYFIAAGVLMNSDITINNIFKNSKQGDREIVNIVKKMGAPIIEEEDKIIIKGP 300

Query: 301 YKLKGIDIDVKDTPDLVPTIAILGCFAEGTTTIYNGEHVRLKECDRLMACAKELTKMGAK 360
           YKLKGIDIDVKDTPDLVPTIAILGCFAEGTTTIYNGEHVRLKECDRLMACAKELTKMGAK
Sbjct: 301 YKLKGIDIDVKDTPDLVPTIAILGCFAEGTTTIYNGEHVRLKECDRLMACAKELTKMGAK 360

Query: 361 ITEKPDGLIIEGVGKLNGAEMETYHDHRLVMAFTVAGMMAEGKTIIKGEDAVKISFPNFV 420
           ITEKPDGLIIEGVGKLNGAEMETYHDHRLVMAFTVAGMMAEGKTIIKGEDAVKISFPNFV
Sbjct: 361 ITEKPDGLIIEGVGKLNGAEMETYHDHRLVMAFTVAGMMAEGKTIIKGEDAVKISFPNFV 420

Query: 421 EAIKSIGANITIK 433
           EAIKSIGANITIK
Sbjct: 421 EAIKSIGANITIK 433


Lambda     K      H
   0.316    0.134    0.376 

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: 883
Number of extensions: 21
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: 433
Length of database: 433
Length adjustment: 32
Effective length of query: 401
Effective length of database: 401
Effective search space:   160801
Effective search space used:   160801
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: 51 (24.3 bits)

Align candidate WP_011972873.1 MAEO_RS00750 (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.18539.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-145  470.7   0.2   2.2e-145  470.5   0.2    1.0  1  lcl|NCBI__GCF_000017185.1:WP_011972873.1  MAEO_RS00750 3-phosphoshikimate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017185.1:WP_011972873.1  MAEO_RS00750 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  470.5   0.2  2.2e-145  2.2e-145       1     414 [.      12     428 ..      12     429 .. 0.97

  Alignments for each domain:
  == domain 1  score: 470.5 bits;  conditional E-value: 2.2e-145
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg.lk 67 
                                               g i++p+sKS++hRa++ a+La+g++++  +L+s+D+l++++   +lGa++   +k+++v+ g+++ +k
  lcl|NCBI__GCF_000017185.1:WP_011972873.1  12 GTINAPPSKSYTHRAVICASLADGTSEIISPLNSADCLSSVHGAMMLGAEIDaTDKNKWVVVGNNNsPK 80 
                                               789*************************************************555********9999** PP

                                 TIGR01356  68 epeaeldlgnsGttaRlltgvlalas.gevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                               +p++++d+gnsGtt+R+ltg++++++ g  +ltgd s+  RP+++l++aL++lg++  s++++g++P+ 
  lcl|NCBI__GCF_000017185.1:WP_011972873.1  81 TPNNVVDIGNSGTTLRILTGIASQIPeGYAILTGDSSIITRPMQPLLDALNQLGIRAFSSKTDGTAPII 149
                                               *************************999***************************************** PP

                                 TIGR01356 136 isgp.lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203
                                               ++ + +k ++v+++g++SsQ++++l+++ p ++ ++t+e+++ +l+s py++it+++l++fgv++e+ +
  lcl|NCBI__GCF_000017185.1:WP_011972873.1 150 VEHGeIKNNVVKIRGDMSSQFITSLMMTMPFSKMDSTIELTT-PLKSAPYLDITIDVLDKFGVKIEKVK 217
                                               *8665999**********************999999999999.*********************99877 PP

                                 TIGR01356 204 e....rkivvkggqkykqkevevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGa 268
                                               +    +k+++kg+qkyk+ +++vegD SsA++f+aa+++ ++++t++n+ +ns+qgd++i++++++mGa
  lcl|NCBI__GCF_000017185.1:WP_011972873.1 218 NknklTKFIIKGNQKYKPYSYTVEGDCSSASYFIAAGVLMNSDITINNIFKNSKQGDREIVNIVKKMGA 286
                                               7667889************************************************************** PP

                                 TIGR01356 269 dveveeqrdvevegasklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiae 337
                                                +  ee+ +++++g+ klkg++  idv++++D++pt+a+l++fAeg+t+i+n e++R+kE+dR+ a+a+
  lcl|NCBI__GCF_000017185.1:WP_011972873.1 287 PIIEEED-KIIIKGPYKLKGID--IDVKDTPDLVPTIAILGCFAEGTTTIYNGEHVRLKECDRLMACAK 352
                                               **99999.7*************..********************************************* PP

                                 TIGR01356 338 eLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFf 406
                                               eL+k+G++++e++dgl+ieG   +l+ga+++ty+DHR++ma++v+g+ aeg+++i+++ +v++sfP+F+
  lcl|NCBI__GCF_000017185.1:WP_011972873.1 353 ELTKMGAKITEKPDGLIIEGV-GKLNGAEMETYHDHRLVMAFTVAGMMAEGKTIIKGEDAVKISFPNFV 420
                                               *********************.7********************************************** PP

                                 TIGR01356 407 evleqlga 414
                                               e+++++ga
  lcl|NCBI__GCF_000017185.1:WP_011972873.1 421 EAIKSIGA 428
                                               ****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (433 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.32
//
[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