Alignments for a candidate for aroB in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Bacteroides thetaiotaomicron VPI-5482

Align 3-dehydroquinate synthase; DHQS; EC 4.2.3.4 (uncharacterized)
to candidate 353501 BT3975 3-dehydroquinate synthase (NCBI ptt file)

Query= curated2:A6LEZ7
         (353 letters)



>FitnessBrowser__Btheta:353501
          Length = 353

 Score =  407 bits (1046), Expect = e-118
 Identities = 196/353 (55%), Positives = 261/353 (73%)

Query: 1   MSEQKVVICKDLKSELQDFLSSLKYDKLFILMDTNTKEKCFPLVEDIPAFQKAPILVMEA 60
           MS+Q+V++C+ L++ L   +    +DKLFIL D +T+  C P ++++   + A  + + A
Sbjct: 1   MSKQEVILCESLETSLGRAIERCPHDKLFILTDEHTQRLCLPSLKEVSFLKDAVEICIGA 60

Query: 61  GDMNKGFVSLAQIWTALSNEGASRNSLLVNLGGGMITDMGGFAGATFKRGIRTINIPTTL 120
            D++K   +LA +W ALS +GA+R+SLL+NLGGGM+TD+GGFA ATFKRGI  INIPTTL
Sbjct: 61  EDVHKTLETLASVWMALSQQGATRHSLLINLGGGMVTDLGGFAAATFKRGISYINIPTTL 120

Query: 121 MASVDAAVGGKTGINFNGLKNEVGSFYPPLCVFIDCDFLRTLDRDNILSGYAEMIKHGLI 180
           +A VDA+VGGKTGINFNGLKNE+GSF P   V I+ +FLR+LD  N  SGYAEM+KHGLI
Sbjct: 121 LAMVDASVGGKTGINFNGLKNEIGSFAPADSVLIETEFLRSLDAQNFFSGYAEMLKHGLI 180

Query: 181 SSMENYASVMLFDIDTMNYSYLNSLVGQSVAVKERIVEEDPKEQGIRKALNFGHTIGHAF 240
           S+  ++  ++ F+ + ++Y+YL ++VG+SV VKE IVE+DP E GIRKALN GHT GHAF
Sbjct: 181 SNTAHWVELLDFNTNNIDYAYLKNMVGRSVQVKEDIVEQDPFEHGIRKALNLGHTAGHAF 240

Query: 241 ESLSFLKMRPILHGHAVAAGIVSELYLSHKLCGFPMEKLSQVVYYIKEYYPALFFDCTDY 300
           ESL+  + RP+LHG+AVA GIV ELYLSH   GFP +K+ Q + +IKE Y +  FDC  Y
Sbjct: 241 ESLALAENRPVLHGYAVAWGIVCELYLSHLKVGFPKDKMRQTIQFIKENYGSFAFDCKQY 300

Query: 301 DTLYELMTHDKKNEGGIINFTLLKNVGDVRINQSVTKEKILESLDFYRESFGI 353
           + LY  M HDKKN  G +NFTLLK +GD+ INQ+  K+ I E LDFYRE  G+
Sbjct: 301 EQLYAFMQHDKKNTSGTVNFTLLKEIGDICINQTADKDTIFEMLDFYRECMGV 353


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: 394
Number of extensions: 10
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: 353
Length of database: 353
Length adjustment: 29
Effective length of query: 324
Effective length of database: 324
Effective search space:   104976
Effective search space used:   104976
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 353501 BT3975 (3-dehydroquinate synthase (NCBI ptt file))
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.3384.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.8e-102  329.0   0.0     2e-102  328.9   0.0    1.0  1  lcl|FitnessBrowser__Btheta:353501  BT3975 3-dehydroquinate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:353501  BT3975 3-dehydroquinate synthase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  328.9   0.0    2e-102    2e-102       5     341 ..       8     342 ..       4     345 .. 0.93

  Alignments for each domain:
  == domain 1  score: 328.9 bits;  conditional E-value: 2e-102
                          TIGR01357   5 vgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldqlleek 79 
                                        + e+l ++l +++++  ++kl+++tde++++l+   l+e+       + ++ + + + +K+let+a+++ +l +++
  lcl|FitnessBrowser__Btheta:353501   8 LCESLETSLGRAIERcPHDKLFILTDEHTQRLCLPSLKEVSF--LKDAVEICIGAEDVHKTLETLASVWMALSQQG 81 
                                        5555556788888887779*******************9994..6899999************************* PP

                          TIGR01357  80 lerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPkaVlidlk 155
                                        ++r+s+l+++GGG v+Dl+GF+Aat++RGi+++++PTtllamvD+svGGKtgin+++ kN iG+f   + Vli+++
  lcl|FitnessBrowser__Btheta:353501  82 ATRHSLLINLGGGMVTDLGGFAAATFKRGISYINIPTTLLAMVDASVGGKTGINFNGLKNEIGSFAPADSVLIETE 157
                                        **************************************************************************** PP

                          TIGR01357 156 vletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDekesglRalL 231
                                        +l++l+ +++ +G+aE++Khgli++ + + el +++   ++  + + l++++ rs++vK+++Ve+D+ e+g+R++L
  lcl|FitnessBrowser__Btheta:353501 158 FLRSLDAQNFFSGYAEMLKHGLISNTAHWVELLDFNT--NN-IDYAYLKNMVGRSVQVKEDIVEQDPFEHGIRKAL 230
                                        ********************************99987..43.4679****************************** PP

                          TIGR01357 232 NfGHtlgHaiEallkyk...lsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklkkklsveellk 304
                                        N+GHt gHa E+l+  +   + HG aVa+G+v+e++ls+ +  +++++++++++++k+ +  + +  + ++e+l++
  lcl|FitnessBrowser__Btheta:353501 231 NLGHTAGHAFESLALAEnrpVLHGYAVAWGIVCELYLSHLKVGFPKDKMRQTIQFIKENYGSFAFD-CKQYEQLYA 305
                                        ***********987666679***********************************99987666666.7******** PP

                          TIGR01357 305 allkDKKnegskiklvlleeiGkaalasevteeelle 341
                                        ++++DKKn ++++++ ll+eiG++ ++++ +++++ e
  lcl|FitnessBrowser__Btheta:353501 306 FMQHDKKNTSGTVNFTLLKEIGDICINQTADKDTIFE 342
                                        **************************98777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (353 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: 10.53
//
[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