GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroD in Salinicoccus carnicancri Crm

Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_017547915.1 C792_RS0102765 type I 3-dehydroquinate dehydratase

Query= BRENDA::P36923
         (253 letters)



>NCBI__GCF_000330705.1:WP_017547915.1
          Length = 253

 Score =  160 bits (404), Expect = 3e-44
 Identities = 88/248 (35%), Positives = 140/248 (56%), Gaps = 4/248 (1%)

Query: 6   VKNVRIGEGNPKIVVPIVAPTAEDILAEATASQTLD--CDLVEWRLDYYENVADFSDVCN 63
           +K+V IGEG PK+VV     T E+I AE   ++T     D+VE R D ++ + +  D   
Sbjct: 3   IKDVTIGEGQPKVVVSFTGHTPEEIRAEIAEARTNSDKFDIVEIRSDSFDAM-NHEDHFA 61

Query: 64  LSQQVMERLGQKPLLLTFRTQKEGGEMAFSEENYFALYHELVKKGALDLLDIELFANPLA 123
           +   +   +G  P++ T+RT  EGG    S   Y +L    +    +D++DIE F     
Sbjct: 62  VVDHISREMGDYPIIYTYRTNGEGGNGTKSAAEYQSLLSHAIDHSEIDIVDIEFFMYEEI 121

Query: 124 ADTLIHEAKKAGIKIVLCNHDFQKTPSQEEIVARLRQMQMRQADICKIAVMPQDATDVLT 183
            D L+  AK+ G+ ++L  HDF+ TP  E+++A  + M  R  DI K+A  P D  DVL+
Sbjct: 122 VDQLVARAKEKGVAVLLSQHDFRDTPHFEDMMATYKNMYERGGDILKLAYQPADGRDVLS 181

Query: 184 LLSATNEMYTHYASVPIVTMSMGQLGMISRVTGQLFGSALTFGSAQQASAPGQLSVQVLR 243
           +LSA ++    + +  +V ++MG+ G I+RV G +FGS LT+G     +APGQ++  +L+
Sbjct: 182 VLSAVHDARRKF-NCQVVGIAMGEAGKITRVAGGVFGSCLTYGHLVNQAAPGQINAGILK 240

Query: 244 NYLKTFEQ 251
            YL  FE+
Sbjct: 241 EYLNIFEE 248


Lambda     K      H
   0.319    0.133    0.374 

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: 139
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: 253
Length of database: 253
Length adjustment: 24
Effective length of query: 229
Effective length of database: 229
Effective search space:    52441
Effective search space used:    52441
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: 46 (22.3 bits)

Align candidate WP_017547915.1 C792_RS0102765 (type I 3-dehydroquinate dehydratase)
to HMM TIGR01093 (aroD: 3-dehydroquinate dehydratase, type I (EC 4.2.1.10))

# 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/TIGR01093.hmm
# target sequence database:        /tmp/gapView.3486334.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01093  [M=229]
Accession:   TIGR01093
Description: aroD: 3-dehydroquinate dehydratase, type I
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.2e-60  189.7   0.0    4.6e-60  189.5   0.0    1.0  1  NCBI__GCF_000330705.1:WP_017547915.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330705.1:WP_017547915.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.5   0.0   4.6e-60   4.6e-60       2     228 ..      15     242 ..      14     243 .. 0.93

  Alignments for each domain:
  == domain 1  score: 189.5 bits;  conditional E-value: 4.6e-60
                             TIGR01093   2 ilvpltakdleealeelekik..evgaDivElRvDllkdvsseksveavaeqlsellkdlplilTiRtqkeGG 72 
                                           ++v+ t ++ ee+ +e+ +++     +DivE+R D+++ +++e+   av++++s  + d+p+i T+Rt+ eGG
  NCBI__GCF_000330705.1:WP_017547915.1  15 VVVSFTGHTPEEIRAEIAEARtnSDKFDIVEIRSDSFDAMNHED-HFAVVDHISREMGDYPIIYTYRTNGEGG 86 
                                           567777777777777666665323569***********999985.88999999999***************** PP

                             TIGR01093  73 kfkgdeeerleelkeaieknlvdlvDiElkleeeavkelikeakkaktkiilSnHdfektpskeelverleka 145
                                           +  +++ e+  +l++ai+++ +d+vDiE ++ ee+v++l++ ak++++ ++lS+Hdf+ tp  e++++ ++++
  NCBI__GCF_000330705.1:WP_017547915.1  87 NGTKSAAEYQSLLSHAIDHSEIDIVDIEFFMYEEIVDQLVARAKEKGVAVLLSQHDFRDTPHFEDMMATYKNM 159
                                           ************************************************************************* PP

                             TIGR01093 146 qsldaDivKiavmaksieDvltLleitlkveeekdkplialsMgekGkisRvlgavlgsvltfgslgkasAPG 218
                                           ++ ++Di+K+a  + + +Dvl +l++   ++++ + +++++ Mge Gki+Rv+g v+gs lt+g+l +++APG
  NCBI__GCF_000330705.1:WP_017547915.1 160 YERGGDILKLAYQPADGRDVLSVLSAVHDARRKFNCQVVGIAMGEAGKITRVAGGVFGSCLTYGHLVNQAAPG 232
                                           ******************************9888*************************************** PP

                             TIGR01093 219 Qisvkelrel 228
                                           Qi+   l+e+
  NCBI__GCF_000330705.1:WP_017547915.1 233 QINAGILKEY 242
                                           **99988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (229 nodes)
Target sequences:                          1  (253 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.15
//
[ok]

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

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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:

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:

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:

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:

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