GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisH in Echinicola vietnamensis KMM 6221, DSM 17526

Align IGP synthase glutamine amidotransferase subunit; EC 2.4.2.- (characterized)
to candidate Echvi_2514 Echvi_2514 imidazole glycerol phosphate synthase, glutamine amidotransferase subunit

Query= CharProtDB::CH_024511
         (196 letters)



>lcl|FitnessBrowser__Cola:Echvi_2514 Echvi_2514 imidazole glycerol
           phosphate synthase, glutamine amidotransferase subunit
          Length = 194

 Score =  144 bits (363), Expect = 1e-39
 Identities = 83/197 (42%), Positives = 116/197 (58%), Gaps = 4/197 (2%)

Query: 1   MNVVILDTGCANLNSVKSAIARHGYEPKVSRDPDVVLLADKLFLPGVGTAQAAMDQVRER 60
           M+V I+     N+ SV  A+ R G    ++ D + +  ADK+  PG G A +AM  +RER
Sbjct: 1   MDVAIIKYNSGNVLSVLYALERLGINANLTDDVEEIKKADKVIFPGQGEASSAMRYLRER 60

Query: 61  ELFDLIKACTQPVLGICLGMQLLGRRSEESNGVDLLGIIDEDVPKMTDFGLPLPHMGWNR 120
            L  LIK   QP  GICLG QLL   SEE N  + LG+    V K       +PH+GWN 
Sbjct: 61  NLDQLIKDLKQPFFGICLGQQLLCEYSEE-NDTECLGVFPVKVRKFPPAD-KVPHVGWNS 118

Query: 121 VYPQAGNRLFQGIEDGAYFYFVHSYAMPVNP-WTIAQCNYGEPFTAAVQKDNFYGVQFHP 179
           +    G +L +GI    Y Y+VHSY   ++P +T+A+ +Y E F+A +QKDNFY +Q HP
Sbjct: 119 LQETQG-QLLEGINTHDYVYYVHSYFAEIHPEFTVAKTHYIEDFSALLQKDNFYAMQAHP 177

Query: 180 ERSGAAGAKLLKNFLEM 196
           E+S  +G K+L NFL++
Sbjct: 178 EKSSHSGQKILTNFLKL 194


Lambda     K      H
   0.322    0.140    0.432 

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: 117
Number of extensions: 6
Number of successful extensions: 4
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: 196
Length of database: 194
Length adjustment: 20
Effective length of query: 176
Effective length of database: 174
Effective search space:    30624
Effective search space used:    30624
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 (21.9 bits)
S2: 44 (21.6 bits)

Align candidate Echvi_2514 Echvi_2514 (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.10528.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
    4.9e-64  201.8   0.0    5.5e-64  201.7   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2514  Echvi_2514 imidazole glycerol ph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2514  Echvi_2514 imidazole glycerol phosphate synthase, glutamine amidotransferase sub
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.7   0.0   5.5e-64   5.5e-64       1     197 [.       3     193 ..       3     194 .] 0.96

  Alignments for each domain:
  == domain 1  score: 201.7 bits;  conditional E-value: 5.5e-64
                            TIGR01855   1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkpv 74 
                                          +++i y++gN+ sv  aler+g ++++++d +e++kadk+++PG G++++am+ lre++l++l   ++  k+p+
  lcl|FitnessBrowser__Cola:Echvi_2514   3 VAIIKYNSGNVLSVLYALERLGINANLTDDVEEIKKADKVIFPGQGEASSAMRYLRERNLDQL---IKDLKQPF 73 
                                          79*******************************************************996655...89999*** PP

                            TIGR01855  75 lgiClGmQllfekseEgkevkglglikgkvkkleaekkvPhiGWnevevvkesellkgleeearvYfvHsYave 148
                                           giClG Qll e seE +++++lg+++ kv+k+  + kvPh+GWn+++ ++ + ll+g++++++vY+vHsY +e
  lcl|FitnessBrowser__Cola:Echvi_2514  74 FGICLGQQLLCEYSEE-NDTECLGVFPVKVRKFPPADKVPHVGWNSLQETQGQ-LLEGINTHDYVYYVHSYFAE 145
                                          ****************.579*************************99988776.******************** PP

                            TIGR01855 149 leeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197
                                          ++  e ++ak++y e+f a+++kdn++++Q HPEkS++ G+k+l nfl+
  lcl|FitnessBrowser__Cola:Echvi_2514 146 IHP-EFTVAKTHYIEDFSALLQKDNFYAMQAHPEKSSHSGQKILTNFLK 193
                                          **8.8******************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (198 nodes)
Target sequences:                          1  (194 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: 5.32
//
[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