Align imidazole glycerol-phosphate synthase (subunit 1/2) (EC 4.3.2.10) (characterized)
to candidate SMc02572 SMc02572 imidazole glycerol phosphate synthase subunit HisH
Query= BRENDA::Q5NMD4 (213 letters) >FitnessBrowser__Smeli:SMc02572 Length = 216 Score = 190 bits (483), Expect = 1e-53 Identities = 105/216 (48%), Positives = 133/216 (61%), Gaps = 13/216 (6%) Query: 9 VALIDYGAGNLRSVANAL----LASGLARENLVVTANPDEVLQADRVVLPGVGAFASCMQ 64 VA+IDYG+GNLRS A +G+A E + +T P+ V ADR+VLPGVGA+A C + Sbjct: 3 VAIIDYGSGNLRSATKAFERAAREAGIAAE-IDLTDRPERVATADRIVLPGVGAYADCRR 61 Query: 65 ALKAIPDMVPALEKAVLEKGRPFLGICVGMQLLADQGEEYGVHQGLGWIKGKVTPLRPND 124 L + M AL +AV + GRPF GICVGMQL++ +G E V +G GWI G V + P D Sbjct: 62 GLAVVEGMEEALTEAVEKTGRPFFGICVGMQLMSSRGLEKTVTKGFGWIAGDVVGMTPED 121 Query: 125 PSCKVPHMGWNQIGLTTDSHPL---LRAGE----AYFLHSYAFVPEDESTLLATTEHGGL 177 PS K+P +GWN + L HPL + GE AYF+HSY E ++A +GG Sbjct: 122 PSLKIPQIGWNTLDLKR-PHPLFDGIPTGENGLHAYFVHSYHLAAERAEDVVAEAGYGGP 180 Query: 178 VTAAVGRDNIMGVQFHPEKSQSYGLEFLSRFLDWNP 213 VTA V RDN G QFHPEKSQ+ GL +S FL W P Sbjct: 181 VTAFVARDNKAGSQFHPEKSQALGLALISNFLRWKP 216 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: 174 Number of extensions: 13 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: 213 Length of database: 216 Length adjustment: 22 Effective length of query: 191 Effective length of database: 194 Effective search space: 37054 Effective search space used: 37054 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 SMc02572 SMc02572 (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.5488.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-60 188.7 0.0 6e-60 188.5 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SMc02572 SMc02572 imidazole glycerol phos Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc02572 SMc02572 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 188.5 0.0 6e-60 6e-60 1 197 [. 3 213 .. 3 214 .. 0.90 Alignments for each domain: == domain 1 score: 188.5 bits; conditional E-value: 6e-60 TIGR01855 1 ivvidygvgNlksvkkalervgaesev......vkdskelekadklvlPGVGafkeamkklrele..lellaekv 67 +++idyg+gNl+s +ka+er+ e+ + ++ +++ +ad++vlPGVGa++++ + l e +e+l+e v lcl|FitnessBrowser__Smeli:SMc02572 3 VAIIDYGSGNLRSATKAFERAAREAGIaaeidlTDRPERVATADRIVLPGVGAYADCRRGLAVVEgmEEALTEAV 77 79***********9999998765544311111155668999******************999887767889999* PP TIGR01855 68 vkkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek...kvPhiGWnevevvkesellkgleeea.. 137 +k+++p+ giC+GmQl+ +++ E++ +kg g+i g+v+ ++ e k+P+iGWn+++ ++ ++l+ g+ +++ lcl|FitnessBrowser__Smeli:SMc02572 78 EKTGRPFFGICVGMQLMSSRGLEKTVTKGFGWIAGDVVGMTPEDpslKIPQIGWNTLDLKRPHPLFDGIPTGEng 152 *****************************************998999**********************765422 PP TIGR01855 138 .rvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 ++YfvHsY++ e e+v+a a yg +a v++dn +g QFHPEkS++ Gl+l++nfl+ lcl|FitnessBrowser__Smeli:SMc02572 153 lHAYFVHSYHLAAERAEDVVAEAGYGGPVTAFVARDNKAGSQFHPEKSQALGLALISNFLR 213 279********************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (216 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: 7.67 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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