GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroD in Sulfurihydrogenibium subterraneum DSM 15120

Align 3-dehydroquinate dehydratase; 3-dehydroquinase; EC 4.2.1.10; Type I DHQase; Type I dehydroquinase; DHQ1 (uncharacterized)
to candidate WP_028949847.1 Q385_RS0100825 type I 3-dehydroquinate dehydratase

Query= curated2:B4U701
         (217 letters)



>NCBI__GCF_000619805.1:WP_028949847.1
          Length = 230

 Score =  155 bits (392), Expect = 6e-43
 Identities = 88/223 (39%), Positives = 135/223 (60%), Gaps = 6/223 (2%)

Query: 1   MKIAIPITDENFDEVLLKA--RNADILEFRVDSFTNKDISFVSGLLKKAKENGFETILTI 58
           +K+A+PITD+N ++ L KA   + DI+E R+D F  +D   +  ++KK KE GF  + T+
Sbjct: 2   VKLALPITDDNVEDTLSKALLEDIDIIELRIDQFKIRDFKHILDVIKKVKEKGFIALATV 61

Query: 59  RSEKEGGAYV--ENRVEMFEKLMPLSDYTDIELSSTDIIAYISRLSKEYNKKLIVSYHNF 116
           RS+ EGGA +  E R E+F ++    D  DIE +S  I   +        K +I+SYH+F
Sbjct: 62  RSKLEGGADIPDEGRFEIFSQIADYVDMADIEYTSFKINKQVIDFYHSKGKSVIMSYHDF 121

Query: 117 EMTPANFVIKETIREALRYG-DIPKIALKANSYEDVARLMCSAIDIKTPKIL-ISMGEFG 174
           E TP++  I+  I E+   G DI K A KA S+EDVAR+MC     +   ++ I MGE G
Sbjct: 122 EKTPSDDYIQTIINESKLMGADIVKYAFKARSFEDVARVMCITHKNREKNLVAILMGEIG 181

Query: 175 KISRIAGFIFGSFISYAYLEKPNAPGQLSLEEMLKLKEMFYLR 217
           K+SR+   +FGS I+Y ++ +  APGQL  +++ +L E F ++
Sbjct: 182 KVSRVIAPVFGSLITYTFIGQSFAPGQLEAKKLNELLEFFNIQ 224


Lambda     K      H
   0.320    0.137    0.375 

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: 147
Number of extensions: 9
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: 217
Length of database: 230
Length adjustment: 22
Effective length of query: 195
Effective length of database: 208
Effective search space:    40560
Effective search space used:    40560
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_028949847.1 Q385_RS0100825 (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.2251245.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.1e-52  165.5   0.7    1.2e-52  165.3   0.7    1.0  1  NCBI__GCF_000619805.1:WP_028949847.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000619805.1:WP_028949847.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.3   0.7   1.2e-52   1.2e-52       2     229 .]       4     218 ..       3     218 .. 0.91

  Alignments for each domain:
  == domain 1  score: 165.3 bits;  conditional E-value: 1.2e-52
                             TIGR01093   2 ilvpltakdleealeelekikevgaDivElRvDllkdvsseksveavaeqlsellkdlplilTiRtqkeGGkf 74 
                                            ++p+t++++e+ l+++      + Di+ElR+D++k    + ++  v+++++   k    + T+R++ eGG  
  NCBI__GCF_000619805.1:WP_028949847.1   4 LALPITDDNVEDTLSKALL---EDIDIIELRIDQFKIRDFK-HILDVIKKVK--EKGFIALATVRSKLEGGA- 69 
                                           6789999999999998877...79***********976555.6889999994..57788899*********6. PP

                             TIGR01093  75 kgdeeerleelkeaieknlvdlvDiElkleeeavkelikeakkaktkiilSnHdfektpskeelverlekaqs 147
                                           +  +e r+e  +++++   vd+ DiE ++ +   k++i   + +++ +i+S+Hdfektps + ++ ++++ + 
  NCBI__GCF_000619805.1:WP_028949847.1  70 DIPDEGRFEIFSQIADY--VDMADIEYTSFKI-NKQVIDFYHSKGKSVIMSYHDFEKTPSDDYIQTIINESKL 139
                                           6778899****888875..5******988765.6789999********************************* PP

                             TIGR01093 148 ldaDivKiavmaksieDvltLleitlkveeekdkplialsMgekGkisRvlgavlgsvltfgslgkasAPGQi 220
                                           ++aDivK a +a+s+eDv+++++it k +   +k+l+a+ Mge Gk+sRv++ v+gs +t+  +g+++APGQ+
  NCBI__GCF_000619805.1:WP_028949847.1 140 MGADIVKYAFKARSFEDVARVMCITHKNR---EKNLVAILMGEIGKVSRVIAPVFGSLITYTFIGQSFAPGQL 209
                                           *************************7776...9**************************************** PP

                             TIGR01093 221 svkelrell 229
                                           + k+l+ell
  NCBI__GCF_000619805.1:WP_028949847.1 210 EAKKLNELL 218
                                           ******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (229 nodes)
Target sequences:                          1  (230 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: 15.28
//
[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:

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