Alignments for a candidate for aroB in Kyrpidia tusciae DSM 2912

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Kyrpidia tusciae DSM 2912

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_013075711.1 BTUS_RS08550 3-dehydroquinate synthase

Query= BRENDA::Q3M4V2
         (363 letters)



>NCBI__GCF_000092905.1:WP_013075711.1
          Length = 377

 Score =  257 bits (656), Expect = 4e-73
 Identities = 148/360 (41%), Positives = 223/360 (61%), Gaps = 6/360 (1%)

Query: 4   VINVNLPTQSYEIAIAPASLDQIGQSL--AGLKLGKKVLLVSNPTIFKH-FGKVAVDSLE 60
           V+ V L  + Y I +A  +LDQ G+ +   GL  G   L+V++ T+ +  + +    +L 
Sbjct: 10  VVWVELGDRRYPIVVADGALDQAGKWMREVGLSPGSAQLIVTDETVDRAGYPRRVAAALT 69

Query: 61  AAGFQVASYCLPAGERYKTLNSIQKLYDIALENRLERSSTMVALGGGVIGDMTGFAAATW 120
           A G +V +  +PAGE  K+L    +L++ AL   L+R ST+ A+GGG++GD+ GF AAT+
Sbjct: 70  AEGVRVETAVVPAGEPTKSLEWASRLWEAALAAGLDRRSTIWAVGGGMVGDLAGFVAATY 129

Query: 121 LRGINVVQVPTTLLAMVDSAIGGKTGVNHPHGKNLIGAFHQPRFVLIDPQVLKTLPVREF 180
           +RGI  VQVPTT LA  D+A+GGK  +N P  KN++GAFHQPR VL DP VL +L  R+ 
Sbjct: 130 MRGIAFVQVPTTWLAH-DAAVGGKVAINLPEAKNVVGAFHQPRLVLYDPTVLDSLSTRDV 188

Query: 181 RAGMAEVIKYGVIWDAELFNQLEQSKRLDQLRYIKPELMDAILTRSCQAKADVVGKDEKE 240
            +G+AEV+K+  I DAELF++L  ++R ++L ++       +L RSC  KA VV +DEKE
Sbjct: 189 ASGLAEVVKHACIRDAELFHEL--AERGNELLHLAGPDRGRLLARSCAIKARVVEEDEKE 246

Query: 241 GGLRAILNYGHTVGHAVESLTNYRLLKHGEAVGIGMVAAGQIAVNLGLWQQADADRQNAL 300
            G RA LN+GHT+GH++E+L +YR  +HGEAV +GMV A  ++ +         +R   L
Sbjct: 247 SGARAHLNFGHTLGHSLETLGDYRRYRHGEAVAVGMVFAALLSEDWLGAPPETGERIARL 306

Query: 301 IEKAGLPTKLPAGLDIEGIIEALQLDKKVKDGKVRFVLPTQIGVVTVTDEVTSDHIRQVL 360
           +E  GLP ++P     + +I  +  DKK+  G++ FVL   IG       +  + +R+VL
Sbjct: 307 LEGIGLPVRIPEEFTDDDLIHPMYKDKKMIGGRLTFVLLEDIGRARSVTGIPEEAVRRVL 366


Lambda     K      H
   0.319    0.136    0.388 

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: 352
Number of extensions: 17
Number of successful extensions: 5
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: 363
Length of database: 377
Length adjustment: 30
Effective length of query: 333
Effective length of database: 347
Effective search space:   115551
Effective search space used:   115551
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_013075711.1 BTUS_RS08550 (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.12501.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.5e-112  360.6   0.0   5.5e-112  360.3   0.0    1.0  1  lcl|NCBI__GCF_000092905.1:WP_013075711.1  BTUS_RS08550 3-dehydroquinate sy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092905.1:WP_013075711.1  BTUS_RS08550 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  360.3   0.0  5.5e-112  5.5e-112       1     341 [.      20     364 ..      20     366 .. 0.96

  Alignments for each domain:
  == domain 1  score: 360.3 bits;  conditional E-value: 5.5e-112
                                 TIGR01357   1 ykvkvgegllkklveelae...ka.sklvvitdeevekl.vaekleealkslgvevlvlvvpdgeesKs 64 
                                               y+++v +g+l+++ ++++e   +  s  +++tde+v++  + +++++al + gv+v+++vvp+ge +Ks
  lcl|NCBI__GCF_000092905.1:WP_013075711.1  20 YPIVVADGALDQAGKWMREvglSPgSAQLIVTDETVDRAgYPRRVAAALTAEGVRVETAVVPAGEPTKS 88 
                                               6899*************99775226999*******98763799************************** PP

                                 TIGR01357  65 letvaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtgin 133
                                               le++++l+++ l+++l+r+s++ a+GGG vgDlaGFvAaty+RGi++vqvPTt la+ D++vGGK++in
  lcl|NCBI__GCF_000092905.1:WP_013075711.1  89 LEWASRLWEAALAAGLDRRSTIWAVGGGMVGDLAGFVAATYMRGIAFVQVPTTWLAH-DAAVGGKVAIN 156
                                               *********************************************************.*********** PP

                                 TIGR01357 134 lplgkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelea 202
                                               lp+ kN++Gaf+qP++Vl+d++vl +l++r +++G+aEv+Kh++i daelf+el +  ++ll+l     
  lcl|NCBI__GCF_000092905.1:WP_013075711.1 157 LPEAKNVVGAFHQPRLVLYDPTVLDSLSTRDVASGLAEVVKHACIRDAELFHELAERGNELLHL-AGPD 224
                                               *********************************************************9999986.5599 PP

                                 TIGR01357 203 leelikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklg 270
                                                 +l++rs+ +Ka+vVeeDekesg Ra LNfGHtlgH +E+l +y+ ++HGeaVa+Gmv++a lse   
  lcl|NCBI__GCF_000092905.1:WP_013075711.1 225 RGRLLARSCAIKARVVEEDEKESGARAHLNFGHTLGHSLETLGDYRrYRHGEAVAVGMVFAALLSEDWL 293
                                               9******************************************************************** PP

                                 TIGR01357 271 llkaellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeel 339
                                                +++e  er+++ll+ +glp++++++++ + l++ + kDKK+ g+++++vlle+iG+a + + ++ee++
  lcl|NCBI__GCF_000092905.1:WP_013075711.1 294 GAPPETGERIARLLEGIGLPVRIPEEFTDDDLIHPMYKDKKMIGGRLTFVLLEDIGRARSVTGIPEEAV 362
                                               **********************************************************99988888777 PP

                                 TIGR01357 340 le 341
                                                +
  lcl|NCBI__GCF_000092905.1:WP_013075711.1 363 RR 364
                                               65 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (377 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: 12.50
//
[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