Alignments for a candidate for aroA in Dehalococcoides mccartyi 195

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Dehalococcoides mccartyi 195

Align 3-phosphoshikimate 1-carboxyvinyltransferase; EC 2.5.1.19; 5-enolpyruvylshikimate-3-phosphate synthase; EPSP synthase; EPSPS (uncharacterized)
to candidate WP_010936240.1 DET_RS02510 3-phosphoshikimate 1-carboxyvinyltransferase

Query= curated2:Q3Z992
         (420 letters)



>NCBI__GCF_000011905.1:WP_010936240.1
          Length = 420

 Score =  820 bits (2117), Expect = 0.0
 Identities = 420/420 (100%), Positives = 420/420 (100%)

Query: 1   MKIRLDKSLPGGEIAVPSSKSYTIRGLIAAAQANGQSRIISPLAADDTLASRQVLSGLGI 60
           MKIRLDKSLPGGEIAVPSSKSYTIRGLIAAAQANGQSRIISPLAADDTLASRQVLSGLGI
Sbjct: 1   MKIRLDKSLPGGEIAVPSSKSYTIRGLIAAAQANGQSRIISPLAADDTLASRQVLSGLGI 60

Query: 61  DINTDAEAESWQLTGNTFKKPAGNLFCRESAATLRFMSAVCARLPFECRLLAGHSLMRRP 120
           DINTDAEAESWQLTGNTFKKPAGNLFCRESAATLRFMSAVCARLPFECRLLAGHSLMRRP
Sbjct: 61  DINTDAEAESWQLTGNTFKKPAGNLFCRESAATLRFMSAVCARLPFECRLLAGHSLMRRP 120

Query: 121 MLPLIQALHQLGIEIETRGNTTVIKGGEITRSKVSLPGNISSQYVSALMLMAPACKSGLE 180
           MLPLIQALHQLGIEIETRGNTTVIKGGEITRSKVSLPGNISSQYVSALMLMAPACKSGLE
Sbjct: 121 MLPLIQALHQLGIEIETRGNTTVIKGGEITRSKVSLPGNISSQYVSALMLMAPACKSGLE 180

Query: 181 IHLATPPASLPYLKMTKQTLESFGIKAYTSIDWQEISIPPQPYLPARYRVEGDWSSASSF 240
           IHLATPPASLPYLKMTKQTLESFGIKAYTSIDWQEISIPPQPYLPARYRVEGDWSSASSF
Sbjct: 181 IHLATPPASLPYLKMTKQTLESFGIKAYTSIDWQEISIPPQPYLPARYRVEGDWSSASSF 240

Query: 241 LALGAIAAPLFISNLDTESFQADRIMIKFLSEMGAEVESGQNWVKVSPKPLTAIQADLTH 300
           LALGAIAAPLFISNLDTESFQADRIMIKFLSEMGAEVESGQNWVKVSPKPLTAIQADLTH
Sbjct: 241 LALGAIAAPLFISNLDTESFQADRIMIKFLSEMGAEVESGQNWVKVSPKPLTAIQADLTH 300

Query: 301 SIDLLPALAITAACAKGQSILSGVRQARIKESNRIRAVSQGLSAMGINVTEEDDRLIIEG 360
           SIDLLPALAITAACAKGQSILSGVRQARIKESNRIRAVSQGLSAMGINVTEEDDRLIIEG
Sbjct: 301 SIDLLPALAITAACAKGQSILSGVRQARIKESNRIRAVSQGLSAMGINVTEEDDRLIIEG 360

Query: 361 GMPRGAEIDSLGDHRIAMAFGALGAVTGETCISEAECVSKTYPDFWQKLESLGGKVIKDV 420
           GMPRGAEIDSLGDHRIAMAFGALGAVTGETCISEAECVSKTYPDFWQKLESLGGKVIKDV
Sbjct: 361 GMPRGAEIDSLGDHRIAMAFGALGAVTGETCISEAECVSKTYPDFWQKLESLGGKVIKDV 420


Lambda     K      H
   0.317    0.132    0.381 

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: 808
Number of extensions: 13
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: 420
Length of database: 420
Length adjustment: 32
Effective length of query: 388
Effective length of database: 388
Effective search space:   150544
Effective search space used:   150544
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_010936240.1 DET_RS02510 (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.6503.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-114  367.8   0.0   3.9e-114  367.6   0.0    1.0  1  lcl|NCBI__GCF_000011905.1:WP_010936240.1  DET_RS02510 3-phosphoshikimate 1


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000011905.1:WP_010936240.1  DET_RS02510 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  367.6   0.0  3.9e-114  3.9e-114       1     414 [.      12     414 ..      12     415 .. 0.96

  Alignments for each domain:
  == domain 1  score: 367.6 bits;  conditional E-value: 3.9e-114
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.ee.keelviegvgglk 67 
                                               gei++p+sKS++ R l++aa a+g++++  +L ++Dtla+ ++l+ lG++++ ++  e++  +g++ +k
  lcl|NCBI__GCF_000011905.1:WP_010936240.1  12 GEIAVPSSKSYTIRGLIAAAQANGQSRIISPLAADDTLASRQVLSGLGIDINtDAeAESWQLTGNT-FK 79 
                                               89**************************************************75579*******88.7* PP

                                 TIGR01356  68 epeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlai 136
                                                p   l +++s++t+R++++v a +++e+ l + +sl +RP+ +l++aL++lg+eie + ++     +i
  lcl|NCBI__GCF_000011905.1:WP_010936240.1  80 KPAGNLFCRESAATLRFMSAVCARLPFECRLLAGHSLMRRPMLPLIQALHQLGIEIETRGNT----TVI 144
                                               *********************************************************98865....689 PP

                                 TIGR01356 137 sgp.lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede 204
                                               +g+ ++  +v l g++SsQy+sal+l ap  +++ ++++ + ++ s py+++t ++l+sfg+++  + +
  lcl|NCBI__GCF_000011905.1:WP_010936240.1 145 KGGeITRSKVSLPGNISSQYVSALMLMAPACKSGLEIHLAT-PPASLPYLKMTKQTLESFGIKAYTSID 212
                                               9997888**********************999888888888.***********************9999 PP

                                 TIGR01356 205 .rkivvkggqkykqkevevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGadvev 272
                                                ++i+++++  y + +++vegD SsA+ fla++ai+   + ++nl ++s q+d+ +i  L+emGa+ve 
  lcl|NCBI__GCF_000011905.1:WP_010936240.1 213 wQEISIPPQ-PYLPARYRVEGDWSSASSFLALGAIAA-PLFISNLDTESFQADRIMIKFLSEMGAEVES 279
                                               99****986.59999*********************9.***************77788*********** PP

                                 TIGR01356 273 eeqrdvevegasklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLek 341
                                                ++ +v+v  ++ l +++  +d+ + iD+lp+la+ aa+A+g++ + ++++ R+kEs+Ri+a+ + L++
  lcl|NCBI__GCF_000011905.1:WP_010936240.1 280 GQN-WVKVS-PKPLTAIQ--ADLTHSIDLLPALAITAACAKGQSILSGVRQARIKESNRIRAVSQGLSA 344
                                               ***.9****.88999999..************************************************* PP

                                 TIGR01356 342 lGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevle 410
                                               +G++v+e  d l+ieG+  + +ga++d+ +DHRiama+  lg +   e+ i +aecv+k++P+F++ le
  lcl|NCBI__GCF_000011905.1:WP_010936240.1 345 MGINVTEEDDRLIIEGG--MPRGAEIDSLGDHRIAMAFGALGAVTG-ETCISEAECVSKTYPDFWQKLE 410
                                               *****************..8**********************9996.********************** PP

                                 TIGR01356 411 qlga 414
                                               +lg 
  lcl|NCBI__GCF_000011905.1:WP_010936240.1 411 SLGG 414
                                               9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (420 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: 10.90
//
[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