Alignments for a candidate for aroB in Thiothrix lacustris DSM 21227

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Thiothrix lacustris DSM 21227

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_028489372.1 Q394_RS0111240 3-dehydroquinate synthase

Query= SwissProt::Q8RU74
         (442 letters)



>NCBI__GCF_000621325.1:WP_028489372.1
          Length = 358

 Score =  439 bits (1130), Expect = e-128
 Identities = 219/356 (61%), Positives = 269/356 (75%), Gaps = 5/356 (1%)

Query: 81  VEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPN 140
           + ++LG RSYPI+IG GLL Q +L+  HI G   +VV+NTTVAPLYL      LT     
Sbjct: 4   LNLELGERSYPIHIGQGLLQQAELVTPHIKGNSAVVVSNTTVAPLYLTAVQQMLT----G 59

Query: 141 VTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRG 200
           +   +V LPDGE +KN++ L +++   +ES+ DR+ T +ALGGGV+GDM GYAAASY RG
Sbjct: 60  LKHSTVTLPDGEAYKNLDVLNQIYTHLLESKADRKTTLIALGGGVVGDMAGYAAASYQRG 119

Query: 201 VNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASG 260
           +NFIQIPTT++A VDSSVGGKTG+NHPLGKNMIGAF+QPQCVLIDTDTLNTLPDREL++G
Sbjct: 120 INFIQIPTTLLAMVDSSVGGKTGVNHPLGKNMIGAFHQPQCVLIDTDTLNTLPDRELSAG 179

Query: 261 LAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRA 320
           +AEV+KYGLIRD  F +W + NM  LLARDP A TYAI RSCE+KA+VV+ DE+ESG RA
Sbjct: 180 IAEVVKYGLIRDPAFLQWLDANMDKLLARDPEALTYAIFRSCEHKAEVVAADERESGQRA 239

Query: 321 TLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAK 380
            LNLGHTFGHA+E  +GYG WLHGEAVA G VMA ++S+++GW+    V   + ILQ+A 
Sbjct: 240 LLNLGHTFGHAIEAAMGYGNWLHGEAVATGMVMAAELSQQMGWLAADDVAYTRHILQRAN 299

Query: 381 LPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETL 436
           LP  PP  MT E F   M+VDKKV DG LRLIL+K SLG  + T D+D  AL   L
Sbjct: 300 LPVVPPAQMTGEDFTRYMSVDKKVLDGTLRLILMK-SLGESIVTADFDPAALKRVL 354


Lambda     K      H
   0.318    0.133    0.385 

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: 420
Number of extensions: 9
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: 442
Length of database: 358
Length adjustment: 31
Effective length of query: 411
Effective length of database: 327
Effective search space:   134397
Effective search space used:   134397
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: 50 (23.9 bits)

Align candidate WP_028489372.1 Q394_RS0111240 (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.17620.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.2e-123  396.6   0.0   5.8e-123  396.4   0.0    1.0  1  lcl|NCBI__GCF_000621325.1:WP_028489372.1  Q394_RS0111240 3-dehydroquinate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000621325.1:WP_028489372.1  Q394_RS0111240 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.4   0.0  5.8e-123  5.8e-123       1     340 [.      13     351 ..      13     355 .. 0.96

  Alignments for each domain:
  == domain 1  score: 396.4 bits;  conditional E-value: 5.8e-123
                                 TIGR01357   1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletv 68 
                                               y++++g+gll+++   + + k +++vv+++ +v+ l+ + ++++l   g ++ ++++pdge +K+l+++
  lcl|NCBI__GCF_000621325.1:WP_028489372.1  13 YPIHIGQGLLQQAELVTPHiKGNSAVVVSNTTVAPLYLTAVQQMLT--GLKHSTVTLPDGEAYKNLDVL 79 
                                               689********8755555556699*********************5..8******************** PP

                                 TIGR01357  69 aklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplg 137
                                               +++++ lle+k++rk++l+a+GGGvvgD+aG++Aa+y+RGi+++q+PTtllamvDssvGGKtg+n+plg
  lcl|NCBI__GCF_000621325.1:WP_028489372.1  80 NQIYTHLLESKADRKTTLIALGGGVVGDMAGYAAASYQRGINFIQIPTTLLAMVDSSVGGKTGVNHPLG 148
                                               ********************************************************************* PP

                                 TIGR01357 138 kNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeel 206
                                               kN+iGaf+qP+ Vlid+++l+tlp+rel++G+aEv+K+gli d +++++l  n ++ll ++  eal+ +
  lcl|NCBI__GCF_000621325.1:WP_028489372.1 149 KNMIGAFHQPQCVLIDTDTLNTLPDRELSAGIAEVVKYGLIRDPAFLQWLDANMDKLLARD-PEALTYA 216
                                               *******************************************************999865.5****** PP

                                 TIGR01357 207 ikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllka 274
                                               i+rs+e KaevV++De+esg RalLN+GHt+gHaiEa+++y+ + HGeaVa+Gmv++a+ls+++g l a
  lcl|NCBI__GCF_000621325.1:WP_028489372.1 217 IFRSCEHKAEVVAADERESGQRALLNLGHTFGHAIEAAMGYGnWLHGEAVATGMVMAAELSQQMGWLAA 285
                                               ********************************************************************* PP

                                 TIGR01357 275 ellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeell 340
                                               +++  ++++l++++lp+  + +++ e ++++++ DKK  +++++l+l++++G+ +++ +++  +l+
  lcl|NCBI__GCF_000621325.1:WP_028489372.1 286 DDVAYTRHILQRANLPVVPPAQMTGEDFTRYMSVDKKVLDGTLRLILMKSLGESIVTADFDPAALK 351
                                               *****************************************************9999888666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (358 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.03
//
[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