GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisH in Sphingomonas indica Dd16

Align imidazole glycerol-phosphate synthase (subunit 1/2) (EC 4.3.2.10) (characterized)
to candidate WP_085217753.1 B9N75_RS04735 imidazole glycerol phosphate synthase subunit HisH

Query= BRENDA::Q5NMD4
         (213 letters)



>NCBI__GCF_900177405.1:WP_085217753.1
          Length = 205

 Score =  137 bits (345), Expect = 1e-37
 Identities = 86/206 (41%), Positives = 118/206 (57%), Gaps = 12/206 (5%)

Query: 9   VALIDYGAGNLRSVANALLASGLARENLVVTANPDEVLQADRVVLPGVGAFASCMQALKA 68
           V ++D G GN++SV     A+    E   + ++P  +    R+ LPGVGAF + M AL  
Sbjct: 3   VTIVDCGIGNIKSVERMFQAADATAE---IVSDPASLKDCRRLALPGVGAFDAGMAALN- 58

Query: 69  IPDMVPALEKAVLEKGRPFLGICVGMQLLADQGEEYGVHQGLGWIKGKVTPLR-PNDPSC 127
                 AL++  LE+  P LGIC+GMQLL  +G E G   GLGWI G V  L    + + 
Sbjct: 59  -DGWRAALDQVALERRIPVLGICLGMQLLC-RGSEEGEAAGLGWIAGDVVTLDLGGNAAL 116

Query: 128 KVPHMGWNQIGLTTDSHPLLR--AGEA--YFLHSYAFVPEDESTLLATTEHGGLVTAAVG 183
           ++PHMGW+ +     ++PL+   AGE   Y +H Y  V + E  +LATTE+G     AV 
Sbjct: 117 RLPHMGWSVV-TPARNNPLIPSDAGEQRFYHVHKYRAVCDREEDVLATTEYGTRFVTAVQ 175

Query: 184 RDNIMGVQFHPEKSQSYGLEFLSRFL 209
           RDNI GVQFHPEKS  +GL+ +  FL
Sbjct: 176 RDNIFGVQFHPEKSHRFGLQLMRNFL 201


Lambda     K      H
   0.318    0.136    0.409 

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: 154
Number of extensions: 14
Number of successful extensions: 6
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: 213
Length of database: 205
Length adjustment: 21
Effective length of query: 192
Effective length of database: 184
Effective search space:    35328
Effective search space used:    35328
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)

Align candidate WP_085217753.1 B9N75_RS04735 (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.1985910.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.4e-67  212.7   0.0    2.6e-67  212.5   0.0    1.0  1  NCBI__GCF_900177405.1:WP_085217753.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085217753.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.5   0.0   2.6e-67   2.6e-67       1     197 [.       3     202 ..       3     203 .. 0.95

  Alignments for each domain:
  == domain 1  score: 212.5 bits;  conditional E-value: 2.6e-67
                             TIGR01855   1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkp 73 
                                           ++++d g+gN+ksv++++++++a++e+v+d  +l+++ +l lPGVGaf+++m+ l++  + +l + + +++ p
  NCBI__GCF_900177405.1:WP_085217753.1   3 VTIVDCGIGNIKSVERMFQAADATAEIVSDPASLKDCRRLALPGVGAFDAGMAALNDGWRAALDQVALERRIP 75 
                                           689*****************************************************988899988999999** PP

                             TIGR01855  74 vlgiClGmQllfekseEgkevkglglikgkvkkleaek....kvPhiGWnevevvkesellkgleeearvYfv 142
                                           vlgiClGmQll + seEg e+ glg+i g+v+ l+       ++Ph+GW  v+++++++l+     e+r+Y+v
  NCBI__GCF_900177405.1:WP_085217753.1  76 VLGICLGMQLLCRGSEEG-EAAGLGWIAGDVVTLDLGGnaalRLPHMGWSVVTPARNNPLIPSDAGEQRFYHV 147
                                           *****************6.68************975544567********************99999****** PP

                             TIGR01855 143 HsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197
                                           H Y++++  ee+vla+++yg++fv+av++dni+gvQFHPEkS+++Gl+l++nfl+
  NCBI__GCF_900177405.1:WP_085217753.1 148 HKYRAVCDREEDVLATTEYGTRFVTAVQRDNIFGVQFHPEKSHRFGLQLMRNFLA 202
                                           *****************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (198 nodes)
Target sequences:                          1  (205 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: 13.61
//
[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