Alignments for a candidate for aroB in Thermodesulforhabdus norvegica DSM 9990

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Thermodesulforhabdus norvegica DSM 9990

Align 3-dehydroquinate synthase; DHQS; EC 4.2.3.4 (uncharacterized)
to candidate WP_093392973.1 BM091_RS01600 3-dehydroquinate synthase

Query= curated2:B5YHI4
         (359 letters)



>NCBI__GCF_900114975.1:WP_093392973.1
          Length = 386

 Score =  237 bits (605), Expect = 3e-67
 Identities = 133/343 (38%), Positives = 197/343 (57%), Gaps = 11/343 (3%)

Query: 3   KLRVELG---ERSYEILIDRGNLSLIGERLLRFSISKKIGIISNPKVSELYGQKVISSLQ 59
           KL V L     RSYE++ + G    +   +   S  +++  + +  V  L+G + +++ +
Sbjct: 25  KLNVVLSGGESRSYEVMCESGLHRRLDRIIKDLSRGRRVFCVWDRFVHGLWGHRCLTATE 84

Query: 60  KEGFEPFVILIPDGEHYKDYFWAYHILTQLLEFGFDRGSFLIALGGGVIGDITGFVASIY 119
                   I+    E  K       +  +L+  G DR S L+A+GGGV GD+ GF+ASIY
Sbjct: 85  S-------IVWDASEQNKKLSAVEELARELVRRGADRHSLLVAVGGGVTGDVVGFLASIY 137

Query: 120 MRGISYIQIPTTLLAQVDSSVGGKTAVNHPLGKNMIGTFWQPSLVWIDVDTLESLPEREF 179
           MRGI  +QIPTTL+AQVDSSVGGKT V+ P GKN++GTF QP  V ID D L++L E  F
Sbjct: 138 MRGIPVVQIPTTLVAQVDSSVGGKTGVDLPEGKNLLGTFHQPLWVGIDPDFLQTLSEENF 197

Query: 180 ISGLAEVIKYGVIWDKEFFEFLEINRTKILKKDKDILISIIKRACEIKAEVVSKDERESA 239
             G+AEVIK   I D +   FL  N   IL++  D++  ++ R  EIKA +V +DE+E  
Sbjct: 198 REGMAEVIKTAWIGDADLVRFLLDNSDDILRRRADVMAHVVFRCVEIKAGIVMEDEKEGG 257

Query: 240 LRAILNYGHTIGHAIETLTGYSSYLHGEAISIGMVHEAKLSSMLGFLDKEDFEKIRNILK 299
           +R +LN GHT GHA+E ++ Y +  HG A+++G++    L   LG+LD+E    ++++L 
Sbjct: 258 VRKVLNLGHTFGHAVERISNY-TINHGHAVAMGLICAGILGRQLGYLDREHLNMLKDLLS 316

Query: 300 EFGLPVNLPINMDSSAMLKTILLDKKNIEGKIRMVIPDSIGKM 342
            +GLP  LP       M+     DKK +   +  VIP   GK+
Sbjct: 317 AYGLPTGLPSEYSPDKMMSVFQADKKKVGNSLVFVIPGPPGKV 359


Lambda     K      H
   0.320    0.141    0.401 

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: 369
Number of extensions: 19
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: 359
Length of database: 386
Length adjustment: 30
Effective length of query: 329
Effective length of database: 356
Effective search space:   117124
Effective search space used:   117124
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_093392973.1 BM091_RS01600 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

# 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/TIGR01357.hmm
# target sequence database:        /tmp/gapView.15571.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01357  [M=344]
Accession:   TIGR01357
Description: aroB: 3-dehydroquinate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.6e-107  343.2   0.0     1e-106  343.0   0.0    1.1  1  lcl|NCBI__GCF_900114975.1:WP_093392973.1  BM091_RS01600 3-dehydroquinate s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900114975.1:WP_093392973.1  BM091_RS01600 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  343.0   0.0    1e-106    1e-106       6     339 ..      43     369 ..      38     374 .. 0.91

  Alignments for each domain:
  == domain 1  score: 343.0 bits;  conditional E-value: 1e-106
                                 TIGR01357   6 gegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvakll 72 
                                               ++gl+++l + +++  + ++++ + d+ v+ l +++ + a +        +v  + e++K+l+ v++l 
  lcl|NCBI__GCF_900114975.1:WP_093392973.1  43 ESGLHRRLDRIIKDlsRGRRVFCVWDRFVHGLWGHRCLTATE-------SIVWDASEQNKKLSAVEELA 104
                                               555555555555554334666666666666666666665555.......59999*************** PP

                                 TIGR01357  73 dqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNli 141
                                               ++l++++++r+s+lva+GGGv gD++GF+A++y+RGi++vq+PTtl+a+vDssvGGKtg++lp+gkNl+
  lcl|NCBI__GCF_900114975.1:WP_093392973.1 105 RELVRRGADRHSLLVAVGGGVTGDVVGFLASIYMRGIPVVQIPTTLVAQVDSSVGGKTGVDLPEGKNLL 173
                                               ********************************************************************* PP

                                 TIGR01357 142 GafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrs 210
                                               G+f+qP  V id+++l+tl+e+++reGmaEviK++ i da+l+++l +n++++l++ + ++++++++r+
  lcl|NCBI__GCF_900114975.1:WP_093392973.1 174 GTFHQPLWVGIDPDFLQTLSEENFREGMAEVIKTAWIGDADLVRFLLDNSDDILRR-RADVMAHVVFRC 241
                                               ***************************************************99986.56********** PP

                                 TIGR01357 211 ievKaevVeeDekesglRalLNfGHtlgHaiEallkyklsHGeaVaiGmvveaklseklgllkaeller 279
                                               +e+Ka +V+eDeke g+R++LN+GHt+gHa+E +++y+++HG+aVa+G++++  l ++lg+l++e l+ 
  lcl|NCBI__GCF_900114975.1:WP_093392973.1 242 VEIKAGIVMEDEKEGGVRKVLNLGHTFGHAVERISNYTINHGHAVAMGLICAGILGRQLGYLDREHLNM 310
                                               ********************************************************************* PP

                                 TIGR01357 280 lvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeel 339
                                               l++ll+++glpt l++++s ++++++++ DKK+ g+++ +v++   Gk++ + ++ +++l
  lcl|NCBI__GCF_900114975.1:WP_093392973.1 311 LKDLLSAYGLPTGLPSEYSPDKMMSVFQADKKKVGNSLVFVIPGPPGKVIWK-TIEDKKL 369
                                               *********************************************9999988.7766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (386 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: 00:00:00.01
# Mc/sec: 13.07
//
[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