Alignments for a candidate for aroG in Dehalococcoides mccartyi 195

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Dehalococcoides mccartyi 195

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_010936245.1 DET_RS02535 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::Q9WYH8
         (338 letters)



>NCBI__GCF_000011905.1:WP_010936245.1
          Length = 351

 Score =  265 bits (678), Expect = 1e-75
 Identities = 149/344 (43%), Positives = 209/344 (60%), Gaps = 16/344 (4%)

Query: 2   IVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVES 61
           ++++K  +T E++  V+       LK  ISKG+ RT+IG+IGD++ +    F SL  V+ 
Sbjct: 1   MIIMKKDATPEELENVIAEVRRCGLKTDISKGEFRTIIGLIGDEKSIPFAYFSSLPGVKE 60

Query: 62  VVRVLKPYKLVSREF------HPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAH 115
              V  PYKL+SRE+            I + D+ IG      IAGPC+VE +E LM+ A 
Sbjct: 61  ARMVETPYKLISREYSNLWQAEGLTREIKVKDITIGGDEPVFIAGPCAVESKEALMKIAE 120

Query: 116 FLSELGVKVLRGGAYKPRTSPYSFQGLGEKG-------LEYLREAADKYGMYVVTEALGE 168
                G ++LRGG YKPR+S +SFQGLG  G       L +L+EA +++ M V+TE  GE
Sbjct: 121 GAKMAGAQILRGGVYKPRSSVHSFQGLGSAGKDEATEALSWLKEAGERFEMAVMTEIRGE 180

Query: 169 DDLPKVAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSG 228
                VAEY DI+Q+G+RN  +  LL+      KPV+ KR F  ++EEFL  AEYIA  G
Sbjct: 181 SQADLVAEYVDILQVGSRNMYDQDLLATVARKGKPVMYKRHFGASMEEFLSFAEYIAAEG 240

Query: 229 NTKIILCERGIRTFEKA---TRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSR 285
           N  IILCERGI    K    TR  LD++AVP+  KE++LPI+VDPSH+ GRRDL+  +S 
Sbjct: 241 NKDIILCERGIVPVGKGKNFTRYNLDLAAVPVALKETYLPIMVDPSHATGRRDLIYSMSC 300

Query: 286 AAIAVGAHGIIVEVHPEPEKALSDGKQSLDFELFKELVQEMKKL 329
           AA+A GA+G+++EVH  P +AL D  Q +     KEL+   +++
Sbjct: 301 AAMAAGANGLMIEVHTNPAEALVDASQMITPPELKELINTCRQI 344


Lambda     K      H
   0.318    0.138    0.388 

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: 297
Number of extensions: 11
Number of successful extensions: 4
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: 338
Length of database: 351
Length adjustment: 29
Effective length of query: 309
Effective length of database: 322
Effective search space:    99498
Effective search space used:    99498
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: 49 (23.5 bits)

Align candidate WP_010936245.1 DET_RS02535 (3-deoxy-7-phosphoheptulonate synthase)
to HMM TIGR01361 (aroF: 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

# 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/TIGR01361.hmm
# target sequence database:        /tmp/gapView.23463.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01361  [M=260]
Accession:   TIGR01361
Description: DAHP_synth_Bsub: 3-deoxy-7-phosphoheptulonate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.4e-94  301.5   0.0    3.1e-94  301.1   0.0    1.1  1  lcl|NCBI__GCF_000011905.1:WP_010936245.1  DET_RS02535 3-deoxy-7-phosphohep


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000011905.1:WP_010936245.1  DET_RS02535 3-deoxy-7-phosphoheptulonate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.1   0.0   3.1e-94   3.1e-94      14     258 ..      88     342 ..      74     344 .. 0.94

  Alignments for each domain:
  == domain 1  score: 301.1 bits;  conditional E-value: 3.1e-94
                                 TIGR01361  14 vdvedvkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPysfqGlg.......e 75 
                                               ++v+d++iG++e+++iaGPC+ves+e ++++a+  k aGa++lrGg++kPr s +sfqGlg       +
  lcl|NCBI__GCF_000011905.1:WP_010936245.1  88 IKVKDITIGGDEPVFIAGPCAVESKEALMKIAEGAKMAGAQILRGGVYKPRSSVHSFQGLGsagkdeaT 156
                                               6899*******************************************************9833333334 PP

                                 TIGR01361  76 eglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLkrglaat 144
                                               e+l++lk+a ++++++v+te+  e++ ++vaeyvDilq+G+rnm + +lL +v+++ kPv+ kr ++a 
  lcl|NCBI__GCF_000011905.1:WP_010936245.1 157 EALSWLKEAGERFEMAVMTEIRGESQADLVAEYVDILQVGSRNMYDQDLLATVARKGKPVMYKRHFGAS 225
                                               78******************************************************************* PP

                                 TIGR01361 145 ieewleaaeYilsegnenvilcerGirtfe...katrftldlsavallkklthlPvivDpshaaGrrdl 210
                                               +ee+l+ aeYi++egn+++ilcerGi  +    + tr+ ldl+av+++ k+t lP++vDpsha+Grrdl
  lcl|NCBI__GCF_000011905.1:WP_010936245.1 226 MEEFLSFAEYIAAEGNKDIILCERGIVPVGkgkNFTRYNLDLAAVPVALKETYLPIMVDPSHATGRRDL 294
                                               **************************987533379********************************** PP

                                 TIGR01361 211 vlplakaavavGadgllievhpdPekalsDseqqltpeefkelvkelk 258
                                               + +++ aa+a+Ga+gl+ievh +P++al D++q +tp e+kel++ ++
  lcl|NCBI__GCF_000011905.1:WP_010936245.1 295 IYSMSCAAMAAGANGLMIEVHTNPAEALVDASQMITPPELKELINTCR 342
                                               *******************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (260 nodes)
Target sequences:                          1  (351 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 10.01
//
[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