GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisH in Desulfovibrio vulgaris Hildenborough

Align Imidazole glycerol phosphate synthase subunit HisH; EC 4.3.2.10; IGP synthase glutaminase subunit; EC 3.5.1.2; IGP synthase subunit HisH; ImGP synthase subunit HisH; IGPS subunit HisH (uncharacterized)
to candidate 209219 DVU0285 imidazole glycerol phosphate synthase, glutamine amidotransferase subunit

Query= curated2:C6C1X6
         (212 letters)



>lcl|MicrobesOnline__882:209219 DVU0285 imidazole glycerol phosphate
           synthase, glutamine amidotransferase subunit
          Length = 213

 Score =  321 bits (822), Expect = 7e-93
 Identities = 148/212 (69%), Positives = 175/212 (82%)

Query: 1   MLAILDYKAGNQTSVQRALNKLGIPNQITSDKEVLSKATGIIFPGVGAAGQAMDELTSGG 60
           MLAILDYKAGNQTSV+RAL+ LGIP  IT+D EV+  A G+IFPGVGAAGQAM+EL + G
Sbjct: 1   MLAILDYKAGNQTSVRRALDHLGIPCVITADPEVIQGAAGVIFPGVGAAGQAMNELVTTG 60

Query: 61  LDELLKDLVQQKKPLLGICVGCQILLDYSEENDTQALSVIPGECRLFNPSWEDYEGVPIR 120
           LDE+L+  VQ  +PLLGICVGCQI+LDYS+ENDT+AL +IPGECRLFNP+W D +G PIR
Sbjct: 61  LDEVLRRQVQAGRPLLGICVGCQIMLDYSQENDTKALGIIPGECRLFNPAWTDEDGAPIR 120

Query: 121 VPHMGWNQIELKQDCILFKDIDPEAHFYFVHSYYPAPEEKYIIGETIYGRPFCSLHGREG 180
           VPHMGWN I  ++ C L K I+PEA FYFVHSYYPAP E+Y+I    YG  FC++HG  G
Sbjct: 121 VPHMGWNHIVQRRPCELLKGIEPEAEFYFVHSYYPAPPEEYVIATCTYGAEFCAIHGGPG 180

Query: 181 LWAVQFHPEKSGRPGLKLLSNFYEYCKEVSDA 212
           LWAVQFHPEKSGRPGL+LL+NF+ YC E +DA
Sbjct: 181 LWAVQFHPEKSGRPGLRLLANFHRYCTEAADA 212


Lambda     K      H
   0.319    0.140    0.433 

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: 244
Number of extensions: 8
Number of successful extensions: 1
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: 212
Length of database: 213
Length adjustment: 21
Effective length of query: 191
Effective length of database: 192
Effective search space:    36672
Effective search space used:    36672
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: 45 (21.9 bits)

Align candidate 209219 DVU0285 (imidazole glycerol phosphate synthase, glutamine amidotransferase subunit)
to HMM TIGR01855 (hisH: imidazole glycerol phosphate synthase, glutamine amidotransferase subunit (EC 2.4.2.-))

# 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/TIGR01855.hmm
# target sequence database:        /tmp/gapView.10943.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01855  [M=198]
Accession:   TIGR01855
Description: IMP_synth_hisH: imidazole glycerol phosphate synthase, glutamine amidotransferase subunit
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-60  189.4   0.0    3.5e-60  189.2   0.0    1.0  1  lcl|MicrobesOnline__882:209219  DVU0285 imidazole glycerol phosp


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:209219  DVU0285 imidazole glycerol phosphate synthase, glutamine amidotransferase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.2   0.0   3.5e-60   3.5e-60       2     197 ..       3     204 ..       2     205 .. 0.96

  Alignments for each domain:
  == domain 1  score: 189.2 bits;  conditional E-value: 3.5e-60
                       TIGR01855   2 vvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkpvlgiClG 80 
                                     +++dy++gN +sv++al+++g   ++++d + ++ a  +++PGVGa+ +am++l  ++l+ + +++v++++p+lgiC+G
  lcl|MicrobesOnline__882:209219   3 AILDYKAGNQTSVRRALDHLGIPCVITADPEVIQGAAGVIFPGVGAAGQAMNELVTTGLDEVLRRQVQAGRPLLGICVG 81 
                                     79********************************************************998889*************** PP

                       TIGR01855  81 mQllfekseEgkevkglglikgkvkkleaek........kvPhiGWnevevvkesellkgleeearvYfvHsYavelee 151
                                      Q++++ s+E +++k+lg+i+g+ + ++ +         +vPh+GWn++   + +ellkg+e ea++YfvHsY+  + e
  lcl|MicrobesOnline__882:209219  82 CQIMLDYSQE-NDTKALGIIPGECRLFNPAWtdedgapiRVPHMGWNHIVQRRPCELLKGIEPEAEFYFVHSYYPAPPE 159
                                     **********.579*************987667789999***********************************99987 PP

                       TIGR01855 152 eeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197
                                      e+v+a+++yg++f a+     + +vQFHPEkSg+ Gl+ll nf +
  lcl|MicrobesOnline__882:209219 160 -EYVIATCTYGAEFCAIHGGPGLWAVQFHPEKSGRPGLRLLANFHR 204
                                     .8*****************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (198 nodes)
Target sequences:                          1  (213 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: 5.03
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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