GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisH in Sphingomonas indica Dd16

Align IGP synthase glutamine amidotransferase subunit; EC 2.4.2.- (characterized)
to candidate WP_085217035.1 B9N75_RS00550 imidazole glycerol phosphate synthase subunit HisH

Query= CharProtDB::CH_024511
         (196 letters)



>NCBI__GCF_900177405.1:WP_085217035.1
          Length = 192

 Score =  147 bits (372), Expect = 9e-41
 Identities = 83/193 (43%), Positives = 111/193 (57%), Gaps = 5/193 (2%)

Query: 3   VVILDTGCANLNSVKSAIARHGYEPKVSRDPDVVLLADKLFLPGVGTAQAAMDQVREREL 62
           + I+D GC NL SV++   R G  P  + DP  +  AD++ LPGVG A  AM ++    L
Sbjct: 2   LAIVDLGCGNLGSVRAGFERLGLAPVTTCDPGAIAAADRIVLPGVGAAGYAMARIHALGL 61

Query: 63  FDLIKACTQPVLGICLGMQLLGRRSEESNGVDLLGIIDEDVPKMTDF-GLPLPHMGWNRV 121
            ++I+   QP+LGICLGMQLL  RSEE  G   LGI+   V  +    GLP+PHMGWN +
Sbjct: 62  AEVIQQLRQPLLGICLGMQLLFERSEE-GGTACLGILPGTVRALKSARGLPVPHMGWNSL 120

Query: 122 YPQAGNRLFQGIEDGAYFYFVHSYAMPVNPWTIAQCNYGEPFTAAVQKDNFYGVQFHPER 181
              A      G++ G + YF HS+A   +  T A+  YG    A V  +N +G QFHPER
Sbjct: 121 ---ARAESGFGLDAGDHLYFAHSFACDASAATTAEVVYGRTIAALVASNNVWGAQFHPER 177

Query: 182 SGAAGAKLLKNFL 194
           S   GA+ LK +L
Sbjct: 178 SAEPGARFLKAWL 190


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: 135
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: 196
Length of database: 192
Length adjustment: 20
Effective length of query: 176
Effective length of database: 172
Effective search space:    30272
Effective search space used:    30272
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 WP_085217035.1 B9N75_RS00550 (imidazole glycerol phosphate synthase subunit HisH)
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.1985020.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    9.2e-58  181.4   0.0      1e-57  181.2   0.0    1.0  1  NCBI__GCF_900177405.1:WP_085217035.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085217035.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.2   0.0     1e-57     1e-57       2     196 ..       3     190 ..       2     192 .] 0.93

  Alignments for each domain:
  == domain 1  score: 181.2 bits;  conditional E-value: 1e-57
                             TIGR01855   2 vvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkpv 74 
                                           +++d g+gNl sv+  +er+g  ++ ++d  ++  ad++vlPGVGa+  am++++ l+   lae +++ ++p+
  NCBI__GCF_900177405.1:WP_085217035.1   3 AIVDLGCGNLGSVRAGFERLGLAPVTTCDPGAIAAADRIVLPGVGAAGYAMARIHALG---LAEVIQQLRQPL 72 
                                           79********************************************************...4455789999** PP

                             TIGR01855  75 lgiClGmQllfekseEgkevkglglikgkvkkleaek..kvPhiGWnevevvkesellkgleeearvYfvHsY 145
                                           lgiClGmQllfe+seEg+ + +lg+++g+v+ l+++   +vPh+GWn++  +++     gl++++++Yf Hs+
  NCBI__GCF_900177405.1:WP_085217035.1  73 LGICLGMQLLFERSEEGG-TACLGILPGTVRALKSARglPVPHMGWNSLARAESG---FGLDAGDHLYFAHSF 141
                                           ****************75.79*************99999********77665554...689************ PP

                             TIGR01855 146 aveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfl 196
                                           a   +   a++a + yg+++ a+v+++n+ g+QFHPE+S++ G+++lk +l
  NCBI__GCF_900177405.1:WP_085217035.1 142 ACDASA--ATTAEVVYGRTIAALVASNNVWGAQFHPERSAEPGARFLKAWL 190
                                           *99987..99**************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (198 nodes)
Target sequences:                          1  (192 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: 20.37
//
[ok]

This GapMind analysis is from Jul 26 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