Alignments for a candidate for aroB in Sphingomonas indica Dd16

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Sphingomonas indica Dd16

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_085217445.1 B9N75_RS02905 3-dehydroquinate synthase

Query= BRENDA::P07639
         (362 letters)



>NCBI__GCF_900177405.1:WP_085217445.1
          Length = 373

 Score =  271 bits (692), Expect = 3e-77
 Identities = 163/351 (46%), Positives = 213/351 (60%), Gaps = 6/351 (1%)

Query: 6   VTLGERSYPITIASGLFNEPASFL-PLKSGEQVMLVTNETLAPLYLDKVRGVLEQAGVNV 64
           V L  RSY + IA GL +E    L P     ++++V++ET+      ++   LE+ G+  
Sbjct: 11  VALEARSYDVRIAPGLIDEAGVLLSPYARDGRLVVVSDETVWTAQGQRLTAGLERGGIAP 70

Query: 65  DSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQRGVRF 124
             +++  GE  KS AVL+ +   LL +   R   ++A GGG+VGDL GFAAA  +RG   
Sbjct: 71  LPLLVSPGEVSKSWAVLEDLTNRLLSERIARGDHILAFGGGMVGDLAGFAAAIVKRGCGI 130

Query: 125 IQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELASGLAE 184
           +Q+PT+LL+QVDSSVGGKT +N   GKNMIGAF+QPA+V++D  CL TLP REL +G AE
Sbjct: 131 VQMPTSLLAQVDSSVGGKTGINAAAGKNMIGAFHQPAAVLIDPTCLATLPERELRAGYAE 190

Query: 185 VIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERET-GLRALL 243
           ++KYG+I D  FF W E N  ALL  D  A+A+ I      KA +VA DERET G RALL
Sbjct: 191 LVKYGLIGDADFFAWCEANGAALLAGDLDAIAHAIAVSVAAKAAIVAEDERETLGRRALL 250

Query: 244 NLGHTFGHAIEAEMGYG-NWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRAGL 302
           NLGH+FGHA+EAE GY    LHGEAVAAGM +A R S  LG    A+ +R+   L   GL
Sbjct: 251 NLGHSFGHALEAEAGYSERLLHGEAVAAGMALAFRLSAALGHCGRADAERVAAHLAAVGL 310

Query: 303 PV---NGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHE 350
           P          SA+     ML DKK     + L+L   IG + V  GV+ E
Sbjct: 311 PTTLDEAGSHASAEDLAALMLHDKKASGDALTLVLAHGIGAAFVEHGVAPE 361


Lambda     K      H
   0.320    0.136    0.392 

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: 299
Number of extensions: 10
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: 362
Length of database: 373
Length adjustment: 30
Effective length of query: 332
Effective length of database: 343
Effective search space:   113876
Effective search space used:   113876
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_085217445.1 B9N75_RS02905 (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.677845.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.1e-108  347.6   0.0   5.1e-108  347.3   0.0    1.0  1  NCBI__GCF_900177405.1:WP_085217445.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085217445.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  347.3   0.0  5.1e-108  5.1e-108       1     335 [.      18     359 ..      18     367 .. 0.96

  Alignments for each domain:
  == domain 1  score: 347.3 bits;  conditional E-value: 5.1e-108
                             TIGR01357   1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvakl 71 
                                           y+v +  gl++++   l+   ++ +lvv++de+v +  +++l + l++ g++ l l+v++ge sKs++++++l
  NCBI__GCF_900177405.1:WP_085217445.1  18 YDVRIAPGLIDEAGVLLSPyaRDGRLVVVSDETVWTAQGQRLTAGLERGGIAPLPLLVSPGEVSKSWAVLEDL 90 
                                           689999*****99999999756699***********************9************************ PP

                             TIGR01357  72 ldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGaf 144
                                           +++ll+e + r + ++a+GGG vgDlaGF+Aa+ +RG  +vq+PT+lla+vDssvGGKtgin + gkN+iGaf
  NCBI__GCF_900177405.1:WP_085217445.1  91 TNRLLSERIARGDHILAFGGGMVGDLAGFAAAIVKRGCGIVQMPTSLLAQVDSSVGGKTGINAAAGKNMIGAF 163
                                           ************************************************************************* PP

                             TIGR01357 145 yqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaev 217
                                           +qP aVlid+++l+tlperelr+G+aE++K+gli da++f+++e n ++ll   +l+a++++i+ s+  Ka +
  NCBI__GCF_900177405.1:WP_085217445.1 164 HQPAAVLIDPTCLATLPERELRAGYAELVKYGLIGDADFFAWCEANGAALLA-GDLDAIAHAIAVSVAAKAAI 235
                                           ***********************************************99886.688***************** PP

                             TIGR01357 218 VeeDekes.glRalLNfGHtlgHaiEallkyk..lsHGeaVaiGmvveaklseklgllkaellerlvallkkl 287
                                           V+eDe+e+ g RalLN+GH++gHa+Ea+++y+  l HGeaVa Gm+++++ls +lg++ + ++er++a l ++
  NCBI__GCF_900177405.1:WP_085217445.1 236 VAEDERETlGRRALLNLGHSFGHALEAEAGYSerLLHGEAVAAGMALAFRLSAALGHCGRADAERVAAHLAAV 308
                                           *******************************999*************************************** PP

                             TIGR01357 288 glptklkk...klsveellkallkDKKnegskiklvlleeiGkaalasevt 335
                                           glpt+l +   + s+e l++ +l+DKK++g+ ++lvl++ iG a++++ v 
  NCBI__GCF_900177405.1:WP_085217445.1 309 GLPTTLDEagsHASAEDLAALMLHDKKASGDALTLVLAHGIGAAFVEHGVA 359
                                           *******9999999*****************************99987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (373 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: 17.54
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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