Alignments for a candidate for aroB in Bacillus alkalinitrilicus DSM 22532

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Bacillus alkalinitrilicus DSM 22532

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_078428496.1 BK574_RS09920 3-dehydroquinate synthase

Query= BRENDA::P07639
         (362 letters)



>NCBI__GCF_002019605.1:WP_078428496.1
          Length = 363

 Score =  256 bits (653), Expect = 9e-73
 Identities = 141/348 (40%), Positives = 203/348 (58%), Gaps = 5/348 (1%)

Query: 1   MERIVVTLGERSYPITIASGLFNEPASFLP---LKSGEQVMLVTNETLAPLYLDKVRGVL 57
           ME++ +    + Y + I  G+  +   +LP    +    V+++T++ +APLYL  V+  +
Sbjct: 1   MEQLHINTSSKQYSVWIGEGIRFKWNEYLPNSLQQKSSSVLIITDDHVAPLYLQDVKKHV 60

Query: 58  EQAGVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAAS 117
                 V   ++P GEQ KS      + T  L+    R++ ++ALGGGV+GDL GF AA+
Sbjct: 61  VDQLSEVYEYVVPAGEQSKSFQQYYEIQTYALEIGLDRNSLIIALGGGVIGDLAGFVAAT 120

Query: 118 YQRGVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRE 177
           Y RG+ FIQ+PTTLL+  DSSVGGK  +NH LGKNMIGAF+QP +V+ D + L++LP  E
Sbjct: 121 YMRGIPFIQIPTTLLAH-DSSVGGKVGINHSLGKNMIGAFHQPEAVLYDPEALQSLPLHE 179

Query: 178 LASGLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERET 237
             SG AE IK+ +I D + F W ++N+     + G      + R   +KA VV+ DE+ET
Sbjct: 180 WRSGFAEAIKHSLIWDASLFQWFKDNIVDFTNIKGSLAEQLLLRSIRVKAAVVSEDEKET 239

Query: 238 GLRALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLL 297
           G+RA+LN GHT GHAIE  +GYG   HGEAVA GM+ A R SER           I   L
Sbjct: 240 GIRAILNFGHTLGHAIETGLGYGKITHGEAVAIGMIFAMRVSERYYNI-PLPVDEIKNWL 298

Query: 298 KRAGLPVNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRS 345
            + G   + P ++     L  M +DKK   G +R++L   +G+ EV S
Sbjct: 299 TKLGFKTDIPSQLDVSQLLHTMKKDKKAHKGIIRMVLMKELGRVEVVS 346


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: 253
Number of extensions: 10
Number of successful extensions: 2
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: 363
Length adjustment: 29
Effective length of query: 333
Effective length of database: 334
Effective search space:   111222
Effective search space used:   111222
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_078428496.1 BK574_RS09920 (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.26647.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.1e-124  400.6   0.0   3.5e-124  400.4   0.0    1.0  1  lcl|NCBI__GCF_002019605.1:WP_078428496.1  BK574_RS09920 3-dehydroquinate s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002019605.1:WP_078428496.1  BK574_RS09920 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.4   0.0  3.5e-124  3.5e-124       2     341 ..      14     354 ..      13     357 .. 0.95

  Alignments for each domain:
  == domain 1  score: 400.4 bits;  conditional E-value: 3.5e-124
                                 TIGR01357   2 kvkvgegllkklveelae....kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsle 66 
                                               +v +geg+  k +e+l +    k+s++++itd++v+ l+ + ++++  ++ +ev+++vvp+ge+sKs++
  lcl|NCBI__GCF_002019605.1:WP_078428496.1  14 SVWIGEGIRFKWNEYLPNslqqKSSSVLIITDDHVAPLYLQDVKKHVVDQLSEVYEYVVPAGEQSKSFQ 82 
                                               56677777666666666555325599******************************************* PP

                                 TIGR01357  67 tvaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlp 135
                                               ++ +++++ le +l+r+s+++a+GGGv+gDlaGFvAaty+RGi+++q+PTtlla+ DssvGGK+gin++
  lcl|NCBI__GCF_002019605.1:WP_078428496.1  83 QYYEIQTYALEIGLDRNSLIIALGGGVIGDLAGFVAATYMRGIPFIQIPTTLLAH-DSSVGGKVGINHS 150
                                               *******************************************************.************* PP

                                 TIGR01357 136 lgkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaeleale 204
                                               lgkN+iGaf+qP+aVl+d++ l++lp +e+r+G+aE+iKh+li+da+lf++ ++n  +++++ + + +e
  lcl|NCBI__GCF_002019605.1:WP_078428496.1 151 LGKNMIGAFHQPEAVLYDPEALQSLPLHEWRSGFAEAIKHSLIWDASLFQWFKDNIVDFTNI-KGSLAE 218
                                               ********************************************************999985.77**** PP

                                 TIGR01357 205 elikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgll 272
                                               +l+ rsi+vKa vV+eDeke+g+Ra+LNfGHtlgHaiE+ l+y+ ++HGeaVaiGm++++++se+++++
  lcl|NCBI__GCF_002019605.1:WP_078428496.1 219 QLLLRSIRVKAAVVSEDEKETGIRAILNFGHTLGHAIETGLGYGkITHGEAVAIGMIFAMRVSERYYNI 287
                                               *******************************************99************************ PP

                                 TIGR01357 273 kaellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeelle 341
                                               +   +++++++l klg +t+++++l+v++ll++++kDKK++++ i++vl++e+G++++  +v+ee ++e
  lcl|NCBI__GCF_002019605.1:WP_078428496.1 288 P-LPVDEIKNWLTKLGFKTDIPSQLDVSQLLHTMKKDKKAHKGIIRMVLMKELGRVEVV-SVDEEPIKE 354
                                               *.999****************************************************99.887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (363 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.06
//
[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