GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisH in Flavobacterium glycines Gm-149

Align IGP synthase glutamine amidotransferase subunit; EC 2.4.2.- (characterized)
to candidate WP_066326536.1 BLR17_RS14000 imidazole glycerol phosphate synthase subunit HisH

Query= CharProtDB::CH_024511
         (196 letters)



>NCBI__GCF_900100165.1:WP_066326536.1
          Length = 193

 Score =  158 bits (399), Expect = 7e-44
 Identities = 84/196 (42%), Positives = 120/196 (61%), Gaps = 3/196 (1%)

Query: 1   MNVVILDTGCANLNSVKSAIARHGYEPKVSRDPDVVLLADKLFLPGVGTAQAAMDQVRER 60
           M +VI++ G  N+ S+  AI R G+   ++ +PD +  ADK+  PGVG A  AM  ++E 
Sbjct: 1   MKIVIINYGAGNIQSILFAIERLGFTAVLTNNPDEIKAADKVIFPGVGEASYAMKMLKES 60

Query: 61  ELFDLIKACTQPVLGICLGMQLLGRRSEESNGVDLLGIIDEDVPKMTDFGLPLPHMGWNR 120
            L  LI    QPVLGICLGMQL+   +EE +    LGI D DV K T   + +P MGWN 
Sbjct: 61  GLDTLIPTLKQPVLGICLGMQLMCNHTEEGDTTG-LGIFDVDVTKFTP-KVKVPQMGWNT 118

Query: 121 VYPQAGNRLFQGIEDGAYFYFVHSYAMPVNPWTIAQCNYGEPFTAAVQKDNFYGVQFHPE 180
           +Y    + LF+ + +  Y Y VHS+  P+   TIA  +Y  P+++A++  NFYG QFHPE
Sbjct: 119 IYDLKSD-LFKDVAEKEYMYLVHSFYAPLCEETIATTDYELPYSSALENGNFYGTQFHPE 177

Query: 181 RSGAAGAKLLKNFLEM 196
           +SG  G ++L NFL++
Sbjct: 178 KSGDMGEQILGNFLKL 193


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: 132
Number of extensions: 4
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: 193
Length adjustment: 20
Effective length of query: 176
Effective length of database: 173
Effective search space:    30448
Effective search space used:    30448
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_066326536.1 BLR17_RS14000 (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.1188119.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    7.9e-67  210.9   0.0    8.8e-67  210.8   0.0    1.0  1  NCBI__GCF_900100165.1:WP_066326536.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066326536.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.8   0.0   8.8e-67   8.8e-67       1     197 [.       3     192 ..       3     193 .] 0.96

  Alignments for each domain:
  == domain 1  score: 210.8 bits;  conditional E-value: 8.8e-67
                             TIGR01855   1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkp 73 
                                           iv+i+yg+gN++s+  a+er+g++++++++ +e++ adk+++PGVG+++ amk l+e++l++l   + + k+p
  NCBI__GCF_900100165.1:WP_066326536.1   3 IVIINYGAGNIQSILFAIERLGFTAVLTNNPDEIKAADKVIFPGVGEASYAMKMLKESGLDTL---IPTLKQP 72 
                                           89*********************************************************7777...889999* PP

                             TIGR01855  74 vlgiClGmQllfekseEgkevkglglikgkvkkleaekkvPhiGWnevevvkesellkgleeearvYfvHsYa 146
                                           vlgiClGmQl+ +++eEg +++glg+++ +v+k++ ++kvP++GWn++  +k+ +l+k++ e++++Y vHs++
  NCBI__GCF_900100165.1:WP_066326536.1  73 VLGICLGMQLMCNHTEEG-DTTGLGIFDVDVTKFTPKVKVPQMGWNTIYDLKS-DLFKDVAEKEYMYLVHSFY 143
                                           *****************7.68*************************8887765.5****************** PP

                             TIGR01855 147 veleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197
                                           ++l e  +++a++dy+  + +a+e++n++g+QFHPEkSg++G ++l nfl+
  NCBI__GCF_900100165.1:WP_066326536.1 144 APLCE--ETIATTDYELPYSSALENGNFYGTQFHPEKSGDMGEQILGNFLK 192
                                           ***98..799***************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (198 nodes)
Target sequences:                          1  (193 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: 11.55
//
[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