GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisH in Trichormus variabilis ATCC 29413

Align imidazole glycerol-phosphate synthase (subunit 1/2) (EC 4.3.2.10) (characterized)
to candidate WP_011320708.1 AVA_RS20365 imidazole glycerol phosphate synthase subunit HisH

Query= BRENDA::Q5NMD4
         (213 letters)



>NCBI__GCF_000204075.1:WP_011320708.1
          Length = 211

 Score =  145 bits (366), Expect = 5e-40
 Identities = 88/206 (42%), Positives = 118/206 (57%), Gaps = 12/206 (5%)

Query: 9   VALIDYGAGNLRSVANALLASGLARENLVVTANPDEVLQADRVVLPGVGAFASCMQALKA 68
           VA+IDY  GNL SV   L  +G      ++T +  E+ +AD V+LPGVGAF   +Q+L++
Sbjct: 4   VAVIDYEMGNLHSVCKGLEKAGATP---IITHSHQELTKADAVILPGVGAFDPAVQSLRS 60

Query: 69  IPDMVPALEKAVLEKGRPFLGICVGMQLLADQGEEYGVHQGLGWIKGKVTPLRPNDPSCK 128
                P   K  +  G+PFLGIC+G+Q+L +   E G   GLG IKGKV     ++P   
Sbjct: 61  RDLEQPI--KDTIASGKPFLGICLGLQILFESSAE-GTQPGLGIIKGKVRRFI-SEPGIT 116

Query: 129 VPHMGWNQIGLTTDSHPLLR----AGEAYFLHSYAFVPEDESTLLATTEHGG-LVTAAVG 183
           +PHMGWNQ+ LT     L          YF+HSY   P +     AT  HG   VTAA+ 
Sbjct: 117 IPHMGWNQLELTQPKSILWEHLPPQPWVYFVHSYYVDPVEPQVRAATVTHGTQTVTAAIA 176

Query: 184 RDNIMGVQFHPEKSQSYGLEFLSRFL 209
            +N+M VQFHPEKS + GL+ LS F+
Sbjct: 177 HENLMAVQFHPEKSSNIGLQILSNFV 202


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: 145
Number of extensions: 13
Number of successful extensions: 7
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: 211
Length adjustment: 21
Effective length of query: 192
Effective length of database: 190
Effective search space:    36480
Effective search space used:    36480
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_011320708.1 AVA_RS20365 (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.2802709.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    8.9e-68  214.0   0.0      1e-67  213.8   0.0    1.0  1  NCBI__GCF_000204075.1:WP_011320708.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000204075.1:WP_011320708.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.8   0.0     1e-67     1e-67       1     197 [.       4     203 ..       4     204 .. 0.94

  Alignments for each domain:
  == domain 1  score: 213.8 bits;  conditional E-value: 1e-67
                             TIGR01855   1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkp 73 
                                           ++vidy++gNl+sv k le++ga++ ++++++el+kad+++lPGVGaf+ a+++lr ++le+ ++++ +++kp
  NCBI__GCF_000204075.1:WP_011320708.1   4 VAVIDYEMGNLHSVCKGLEKAGATPIITHSHQELTKADAVILPGVGAFDPAVQSLRSRDLEQPIKDTIASGKP 76 
                                           79*********************************************************888889******** PP

                             TIGR01855  74 vlgiClGmQllfekseEgkevkglglikgkvkkleaek..kvPhiGWnevevvkes.ellkgleeearvYfvH 143
                                           +lgiClG+Q+lfe+s Eg+ ++glg+ikgkv+++ +e   ++Ph+GWn++e ++ +  l + l  +  vYfvH
  NCBI__GCF_000204075.1:WP_011320708.1  77 FLGICLGLQILFESSAEGT-QPGLGIIKGKVRRFISEPgiTIPHMGWNQLELTQPKsILWEHLPPQPWVYFVH 148
                                           *****************75.7*************999999***********98766267789*********** PP

                             TIGR01855 144 sYaveleeeeavlakadyg.ekfvaavekdnivgvQFHPEkSgktGlkllknfle 197
                                           sY+v + e +   a++++g ++ +aa++++n+++vQFHPEkS+++Gl++l+nf++
  NCBI__GCF_000204075.1:WP_011320708.1 149 SYYVDPVEPQVRAATVTHGtQTVTAAIAHENLMAVQFHPEKSSNIGLQILSNFVS 203
                                           ********9999999999725689*****************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (198 nodes)
Target sequences:                          1  (211 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: 17.81
//
[ok]

This GapMind analysis is from Jul 25 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