Alignments for a candidate for aroA in Methanosarcina acetivorans C2A

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Methanosarcina acetivorans C2A

Align 3-phosphoshikimate 1-carboxyvinyltransferase; EC 2.5.1.19; 5-enolpyruvylshikimate-3-phosphate synthase; EPSP synthase; EPSPS (uncharacterized)
to candidate WP_011024417.1 MA_RS23690 3-phosphoshikimate 1-carboxyvinyltransferase

Query= curated2:Q8THH3
         (430 letters)



>NCBI__GCF_000007345.1:WP_011024417.1
          Length = 430

 Score =  826 bits (2134), Expect = 0.0
 Identities = 430/430 (100%), Positives = 430/430 (100%)

Query: 1   MRVSISKSSVKGEVFAPSSKSYTHRAITLAALSNESIVRRPLLSADTLATIRASEMFGAS 60
           MRVSISKSSVKGEVFAPSSKSYTHRAITLAALSNESIVRRPLLSADTLATIRASEMFGAS
Sbjct: 1   MRVSISKSSVKGEVFAPSSKSYTHRAITLAALSNESIVRRPLLSADTLATIRASEMFGAS 60

Query: 61  VKREEENLIIHGFNGKPNVPDDVIDAANSGTTLRLMTAIAGLTDGITVLTGDSSLRTRPN 120
           VKREEENLIIHGFNGKPNVPDDVIDAANSGTTLRLMTAIAGLTDGITVLTGDSSLRTRPN
Sbjct: 61  VKREEENLIIHGFNGKPNVPDDVIDAANSGTTLRLMTAIAGLTDGITVLTGDSSLRTRPN 120

Query: 121 GPLLKTLNQLGASACSTRGNEKAPLVVKGGLEGKKVSIEGSISSQFISALLIACPLAENS 180
           GPLLKTLNQLGASACSTRGNEKAPLVVKGGLEGKKVSIEGSISSQFISALLIACPLAENS
Sbjct: 121 GPLLKTLNQLGASACSTRGNEKAPLVVKGGLEGKKVSIEGSISSQFISALLIACPLAENS 180

Query: 181 TTLSIIGKLKSRPYVDVTIEMLELAGVKIHTDENNGTKFIIPGKQKYDLKEYTIPGDFSS 240
           TTLSIIGKLKSRPYVDVTIEMLELAGVKIHTDENNGTKFIIPGKQKYDLKEYTIPGDFSS
Sbjct: 181 TTLSIIGKLKSRPYVDVTIEMLELAGVKIHTDENNGTKFIIPGKQKYDLKEYTIPGDFSS 240

Query: 241 ASYLLAAAAMTEGSEITVKNLFPSKQGDKLIIETLKQMGADITWDREAGIVTVRGGRKLK 300
           ASYLLAAAAMTEGSEITVKNLFPSKQGDKLIIETLKQMGADITWDREAGIVTVRGGRKLK
Sbjct: 241 ASYLLAAAAMTEGSEITVKNLFPSKQGDKLIIETLKQMGADITWDREAGIVTVRGGRKLK 300

Query: 301 AVTFDAGATPDLVPTVAVLAAVAEGTSRIENAEHVRYKETDRLSALATELPKLGVKLKEE 360
           AVTFDAGATPDLVPTVAVLAAVAEGTSRIENAEHVRYKETDRLSALATELPKLGVKLKEE
Sbjct: 301 AVTFDAGATPDLVPTVAVLAAVAEGTSRIENAEHVRYKETDRLSALATELPKLGVKLKEE 360

Query: 361 KDSLTITGGELKGAEVHGWDDHRIVMSLALAGMVAGNTTIDTTESVAISYPDFFEDMSNL 420
           KDSLTITGGELKGAEVHGWDDHRIVMSLALAGMVAGNTTIDTTESVAISYPDFFEDMSNL
Sbjct: 361 KDSLTITGGELKGAEVHGWDDHRIVMSLALAGMVAGNTTIDTTESVAISYPDFFEDMSNL 420

Query: 421 GVKIKQISEE 430
           GVKIKQISEE
Sbjct: 421 GVKIKQISEE 430


Lambda     K      H
   0.313    0.130    0.355 

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: 775
Number of extensions: 32
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: 430
Length of database: 430
Length adjustment: 32
Effective length of query: 398
Effective length of database: 398
Effective search space:   158404
Effective search space used:   158404
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate WP_011024417.1 MA_RS23690 (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.26721.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.1e-141  456.8   0.2   3.6e-141  456.7   0.2    1.0  1  lcl|NCBI__GCF_000007345.1:WP_011024417.1  MA_RS23690 3-phosphoshikimate 1-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000007345.1:WP_011024417.1  MA_RS23690 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.7   0.2  3.6e-141  3.6e-141       1     413 [.      12     421 ..      12     423 .. 0.98

  Alignments for each domain:
  == domain 1  score: 456.7 bits;  conditional E-value: 3.6e-141
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg.lke 68 
                                               ge+ +p+sKS++hRa+ laaL++ e++v+++L s+Dtlat++a +++Ga+v++e+e+l+i+g++g ++ 
  lcl|NCBI__GCF_000007345.1:WP_011024417.1  12 GEVFAPSSKSYTHRAITLAALSN-ESIVRRPLLSADTLATIRASEMFGASVKREEENLIIHGFNGkPNV 79 
                                               7899******************9.9**************************************99999* PP

                                 TIGR01356  69 peaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlais 137
                                               p++++d++nsGtt+Rl+t+++ l++g +vltgd sl+ RP ++l++ L++lga+ +s+++++++Pl+++
  lcl|NCBI__GCF_000007345.1:WP_011024417.1  80 PDDVIDAANSGTTLRLMTAIAGLTDGITVLTGDSSLRTRPNGPLLKTLNQLGASACSTRGNEKAPLVVK 148
                                               ********************************************************************* PP

                                 TIGR01356 138 gplkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede.. 204
                                               g+l+g++v ++gs+SsQ++sall+a pla++  tl+i+g kl+srpy+++t+++l+ +gv+++ +++  
  lcl|NCBI__GCF_000007345.1:WP_011024417.1 149 GGLEGKKVSIEGSISSQFISALLIACPLAENSTTLSIIG-KLKSRPYVDVTIEMLELAGVKIHTDENng 216
                                               ***************************************.***********************999888 PP

                                 TIGR01356 205 rkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadvev 272
                                               +k++++g+qky  ke++++gD+SsA+++laaaa+t++ e+tv+nl   s+qgdk ii++L++mGad+++
  lcl|NCBI__GCF_000007345.1:WP_011024417.1 217 TKFIIPGKQKYDLKEYTIPGDFSSASYLLAAAAMTEGsEITVKNLFP-SKQGDKLIIETLKQMGADITW 284
                                               9************************************9*******99.99***99999*********** PP

                                 TIGR01356 273 eeqr.dvevegasklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLe 340
                                               +++   v+v+g +klk+v+   d+  ++D++pt+avlaa+Aeg++ri+n+e++R+kE+dR++a+a+eL 
  lcl|NCBI__GCF_000007345.1:WP_011024417.1 285 DREAgIVTVRGGRKLKAVT--FDAGATPDLVPTVAVLAAVAEGTSRIENAEHVRYKETDRLSALATELP 351
                                               *999899************..************************************************ PP

                                 TIGR01356 341 klGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevl 409
                                               klGv+ +e +d+l+i+G+  elkga+v+++dDHRi+m+la++g++a  +++i+ +e va+s+P+Ffe++
  lcl|NCBI__GCF_000007345.1:WP_011024417.1 352 KLGVKLKEEKDSLTITGG--ELKGAEVHGWDDHRIVMSLALAGMVAG-NTTIDTTESVAISYPDFFEDM 417
                                               ******************..7*************************6.********************* PP

                                 TIGR01356 410 eqlg 413
                                                +lg
  lcl|NCBI__GCF_000007345.1:WP_011024417.1 418 SNLG 421
                                               9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (430 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.03
//
[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