Alignments for a candidate for aroB in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Echinicola vietnamensis KMM 6221, DSM 17526

Align 3-dehydroquinate synthase; DHQS; EC 4.2.3.4 (uncharacterized)
to candidate Echvi_0121 Echvi_0121 3-dehydroquinate synthase

Query= curated2:A6LEZ7
         (353 letters)



>FitnessBrowser__Cola:Echvi_0121
          Length = 345

 Score =  272 bits (696), Expect = 8e-78
 Identities = 138/345 (40%), Positives = 214/345 (62%), Gaps = 7/345 (2%)

Query: 4   QKVVICKDLKSELQDFLSSLKYDKLFILMDTNTKEKCFPLV-EDIPAFQKAPILVMEAGD 62
           + ++    +  +L+ FL S  + KL ++ D+NT + C+PL+ E +P  +       EAG+
Sbjct: 2   ESIIFSTQIAPDLERFLKSKNFSKLGVITDSNTSQACYPLIREALPLHEH---FAFEAGE 58

Query: 63  MNKGFVSLAQIWTALSNEGASRNSLLVNLGGGMITDMGGFAGATFKRGIRTINIPTTLMA 122
           +NK   +  +IW  +++ G  R SL++NLGGG+  DMGGF  +T+KRG++ INIPTTL++
Sbjct: 59  VNKNLDTCQKIWQWMTDCGFDRKSLIINLGGGVTGDMGGFCASTYKRGVKFINIPTTLLS 118

Query: 123 SVDAAVGGKTGINFNGLKNEVGSFYPPLCVFIDCDFLRTLDRDNILSGYAEMIKHGLISS 182
            VDA+VGGK G++FNG KN +G F  P  V I   FL +L    + SGYAE++KHGLI +
Sbjct: 119 QVDASVGGKLGVDFNGFKNHIGVFNEPEAVIISAAFLSSLPLPELRSGYAEVLKHGLIRN 178

Query: 183 MENYASVMLFDIDTMNYSYLNSLVGQSVAVKERIVEEDPKEQGIRKALNFGHTIGHAFES 242
              + S+ L + +   ++    ++ +SV +K+ +V +DPKE G+RK LNFGHT+GHA ES
Sbjct: 179 ENYFNSLKLQNWEDQRWT---EIIEKSVYIKKDVVTKDPKEDGLRKILNFGHTVGHAVES 235

Query: 243 LSFLKMRPILHGHAVAAGIVSELYLSHKLCGFPMEKLSQVVYYIKEYYPALFFDCTDYDT 302
                 R +LHG A+A G+++E YLS K    P E+L  +   + E +  +     D D 
Sbjct: 236 FYLDTERHLLHGEAIAIGMIAEAYLSQKHIRLPKEELQSITTALLEVFGKVEIPKEDLDA 295

Query: 303 LYELMTHDKKNEGGIINFTLLKNVGDVRINQSVTKEKILESLDFY 347
           + +L   DKKN+G  IN +LLK +G+   N +V+ + I++SL FY
Sbjct: 296 IAQLCFQDKKNDGKTINCSLLKKIGECDYNIAVSLDDIIDSLHFY 340


Lambda     K      H
   0.321    0.139    0.402 

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: 363
Number of extensions: 14
Number of successful extensions: 3
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: 353
Length of database: 345
Length adjustment: 29
Effective length of query: 324
Effective length of database: 316
Effective search space:   102384
Effective search space used:   102384
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 Echvi_0121 Echvi_0121 (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.8666.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   2.9e-103  331.6   0.0   3.2e-103  331.5   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_0121  Echvi_0121 3-dehydroquinate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0121  Echvi_0121 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  331.5   0.0  3.2e-103  3.2e-103       8     336 ..       9     330 ..       2     338 .. 0.92

  Alignments for each domain:
  == domain 1  score: 331.5 bits;  conditional E-value: 3.2e-103
                            TIGR01357   8 gllkklveelaeka.sklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldqlleekl 80 
                                          ++   l + l++k+ skl vitd+++++ +   ++eal      ++++ +++ge +K+l+t++k+++++ + ++
  lcl|FitnessBrowser__Cola:Echvi_0121   9 QIAPDLERFLKSKNfSKLGVITDSNTSQACYPLIREALPL----HEHFAFEAGEVNKNLDTCQKIWQWMTDCGF 78 
                                          55555666666655699***********999999999965....88999************************* PP

                            TIGR01357  81 erksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPkaVlidl 154
                                          +rks+++++GGGv gD++GF A+ty+RG++++++PTtll++vD+svGGK g+++++ kN iG f +P+aV+i+ 
  lcl|FitnessBrowser__Cola:Echvi_0121  79 DRKSLIINLGGGVTGDMGGFCASTYKRGVKFINIPTTLLSQVDASVGGKLGVDFNGFKNHIGVFNEPEAVIISA 152
                                          ************************************************************************** PP

                            TIGR01357 155 kvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDekesglR 228
                                          ++l++lp  elr+G+aEv+Khgli +++ f+ l+ ++       e + ++e+i++s+ +K++vV++D+ke glR
  lcl|FitnessBrowser__Cola:Echvi_0121 153 AFLSSLPLPELRSGYAEVLKHGLIRNENYFNSLKLQNW------EDQRWTEIIEKSVYIKKDVVTKDPKEDGLR 220
                                          *******************************9998443......3489************************** PP

                            TIGR01357 229 alLNfGHtlgHaiEallkyk...lsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklkkklsv 299
                                          ++LNfGHt+gHa+E+++  +   l HGea+aiGm+ ea+ls+k   l++e+l+++++ l ++  +++++k  ++
  lcl|FitnessBrowser__Cola:Echvi_0121 221 KILNFGHTVGHAVESFYLDTerhLLHGEAIAIGMIAEAYLSQKHIRLPKEELQSITTALLEVFGKVEIPK-EDL 293
                                          **************987555567**********************************************7.9** PP

                            TIGR01357 300 eellkallkDKKnegskiklvlleeiGkaalasevte 336
                                          +++++ + +DKKn+g++i+  ll++iG++  +  v+ 
  lcl|FitnessBrowser__Cola:Echvi_0121 294 DAIAQLCFQDKKNDGKTINCSLLKKIGECDYNIAVSL 330
                                          ****************************988766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (345 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: 11.85
//
[ok]

This GapMind analysis is from Apr 09 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