Alignments for a candidate for aroB in Haloglycomyces albus DSM 45210

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Haloglycomyces albus DSM 45210

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_025274781.1 HALAL_RS0114995 3-dehydroquinate synthase

Query= BRENDA::P9WPX9
         (362 letters)



>NCBI__GCF_000527155.1:WP_025274781.1
          Length = 519

 Score =  345 bits (884), Expect = 2e-99
 Identities = 186/343 (54%), Positives = 229/343 (66%), Gaps = 3/343 (0%)

Query: 17  PYPVVIGTGLLDELEDLLADRHKVAVVHQPGLAETAEEIRKRLAGKGVDAHRIEIPDAEA 76
           PY V IG G    ++++L D  K+A ++ P +     +I   L  +G     +EIPDAEA
Sbjct: 178 PYSVTIGPGTATLVDEVLPDAEKIAFIYSPTVEPQVRDILAALP-QGRRIVTLEIPDAEA 236

Query: 77  GKDLPVVGFIWEVLGRIGIGRKDALVSLGGGAATDVAGFAAATWLRGVSIVHLPTTLLGM 136
           GK+L VVG  WE LG  G  R DA+VS+GGGA +DVAGF AATWLRGV +VHLPT+LLG 
Sbjct: 237 GKELDVVGQCWEALGEEGFTRTDAVVSVGGGAVSDVAGFVAATWLRGVDVVHLPTSLLGA 296

Query: 137 VDAAVGGKTGINTDAGKNLVGAFHQPLAVLVDLATLQTLPRDEMICGMAEVVKAGFIADP 196
           VDAAVGGKTGINT AGKNLVGAFH P AVL D   L+TLPR+EM  G+AE++KAGFI D 
Sbjct: 297 VDAAVGGKTGINTAAGKNLVGAFHPPKAVLCDTRMLRTLPREEMSNGLAEIIKAGFICDT 356

Query: 197 VILDLIEADPQAALDPAGDVLPELIRRAITVKAEVVAADEKESELREILNYGHTLGHAIE 256
            ILDLIE DP  ALDP G ++PEL+RRAI VKA++V  D  E   R  LN+GHTL HAIE
Sbjct: 357 TILDLIEHDPAGALDPNGSLVPELMRRAIAVKADIVGEDLTEQGKRVWLNFGHTLAHAIE 416

Query: 257 RRERYRWRHGAAVSVGLVFAAELARLAGRLDDATAQRHRTILSSLGLPVSYDPDALPQLL 316
           ++ERYR RHG AV++G+V+AAEL  L  R++    +R R IL S+GLP SY       L 
Sbjct: 417 KQERYRLRHGFAVAIGMVYAAELGALTERVN--VTRRLRRILESVGLPTSYSGSDWDSLR 474

Query: 317 EIMAGDKKTRAGVLRFVVLDGLAKPGRMVGPDPGLLVTAYAGV 359
             M  DKK R    RFV+LD +A+P  +      L   A+  V
Sbjct: 475 HAMVVDKKNRGSTQRFVLLDDIAQPAAVSDVPASLQAEAFGKV 517


Lambda     K      H
   0.320    0.139    0.406 

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: 557
Number of extensions: 28
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: 519
Length adjustment: 32
Effective length of query: 330
Effective length of database: 487
Effective search space:   160710
Effective search space used:   160710
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: 51 (24.3 bits)

Align candidate WP_025274781.1 HALAL_RS0114995 (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.3719312.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.6e-107  344.5   0.0   4.2e-105  337.7   0.0    2.0  2  NCBI__GCF_000527155.1:WP_025274781.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000527155.1:WP_025274781.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0   0.00068   0.00068      47      95 ..      41      84 ..      30      85 .. 0.81
   2 !  337.7   0.0  4.2e-105  4.2e-105       1     340 [.     179     511 ..     179     515 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.00068
                             TIGR01357 47 lgvevlvlvvpdgeesKsletvaklldqlleeklerksvlvaiGGGvvg 95
                                          +g++v  + v++ge     +++ +l+++ +++ +  ++ ++++GGG+v+
  NCBI__GCF_000527155.1:WP_025274781.1 41 AGTSVSDIFVNHGE-----DHFRELERKAVAAAIAEHDGVISLGGGAVS 84
                                          56666666666666.....57999***********************95 PP

  == domain 2  score: 337.7 bits;  conditional E-value: 4.2e-105
                             TIGR01357   1 ykvkvgegllkklveelaekasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklld 73 
                                           y+v++g g+ + + e l   a+k+ +i + +ve +v + l+++ +  g ++ +l +pd+e  K+l++v ++++
  NCBI__GCF_000527155.1:WP_025274781.1 179 YSVTIGPGTATLVDEVLP-DAEKIAFIYSPTVEPQVRDILAALPQ--GRRIVTLEIPDAEAGKELDVVGQCWE 248
                                           678899888875555555.689**************877777764..8************************* PP

                             TIGR01357  74 qlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyq 146
                                           +l ee+++r +++v++GGG+v+D+aGFvAat+lRG+++v++PT+ll++vD++vGGKtgin++ gkNl+Gaf+ 
  NCBI__GCF_000527155.1:WP_025274781.1 249 ALGEEGFTRTDAVVSVGGGAVSDVAGFVAATWLRGVDVVHLPTSLLGAVDAAVGGKTGINTAAGKNLVGAFHP 321
                                           ************************************************************************* PP

                             TIGR01357 147 PkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVe 219
                                           PkaVl+d+++l+tlp++e+++G+aE+iK g+i d  +++ +e+  +  l+  + + + el++r+i vKa++V 
  NCBI__GCF_000527155.1:WP_025274781.1 322 PKAVLCDTRMLRTLPREEMSNGLAEIIKAGFICDTTILDLIEHDPAGALD-PNGSLVPELMRRAIAVKADIVG 393
                                           *******************************************9987776.578******************* PP

                             TIGR01357 220 eDekesglRalLNfGHtlgHaiEallkyklsHGeaVaiGmvveaklseklgllkaellerlvallkklglptk 292
                                           eD +e+g R  LNfGHtl+HaiE+   y+l+HG aVaiGmv++a+l   +  ++  +++rl+++l+++glpt+
  NCBI__GCF_000527155.1:WP_025274781.1 394 EDLTEQGKRVWLNFGHTLAHAIEKQERYRLRHGFAVAIGMVYAAELGALTERVN--VTRRLRRILESVGLPTS 464
                                           ***********************************************9999988..9**************** PP

                             TIGR01357 293 lkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeell 340
                                           ++   + ++l +a+  DKKn+gs+ ++vll++i+++a  s+v+++ + 
  NCBI__GCF_000527155.1:WP_025274781.1 465 YSG-SDWDSLRHAMVVDKKNRGSTQRFVLLDDIAQPAAVSDVPASLQA 511
                                           **7.********************************999998876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (519 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: 18.06
//
[ok]

This GapMind analysis is from Jul 25 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 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