Align imidazole glycerol-phosphate synthase (subunit 1/2) (EC 4.3.2.10) (characterized)
to candidate GFF916 PGA1_c09320 imidazole glycerol phosphate synthase subunit HisH
Query= BRENDA::Q5NMD4 (213 letters) >FitnessBrowser__Phaeo:GFF916 Length = 212 Score = 184 bits (468), Expect = 8e-52 Identities = 96/211 (45%), Positives = 130/211 (61%), Gaps = 9/211 (4%) Query: 10 ALIDYGAGNLRSVANALLASGLARE----NLVVTANPDEVLQADRVVLPGVGAFASCMQA 65 A+IDY +GNL S A +ARE ++VT++ D V +ADR+VLPG GAF +C + Sbjct: 4 AIIDYESGNLHSAEKAF--QRMAREVDGGEVMVTSDADVVARADRLVLPGDGAFPACAEE 61 Query: 66 LKAIPDMVPALEKAVLEKGRPFLGICVGMQLLADQGEEYGVHQGLGWIKGKVTPLRPNDP 125 L+ + A+ +AV + GRPFLGICVGMQL+A G EY GLGW++G V + P+D Sbjct: 62 LRGHRGIYEAMVEAVEQNGRPFLGICVGMQLMATTGHEYRDTPGLGWVQGDVVKITPSDS 121 Query: 126 SCKVPHMGWNQIGLTTDS---HPLLRAGEAYFLHSYAFVPEDESTLLATTEHGGLVTAAV 182 + KVPHMGWN + + D + YF+HSY F D + LA ++G VTA + Sbjct: 122 ALKVPHMGWNNLVIDHDHTIFDGITSGDHCYFVHSYHFRVNDPAERLAHVDYGSDVTAVI 181 Query: 183 GRDNIMGVQFHPEKSQSYGLEFLSRFLDWNP 213 GRD ++G+QFHPEKSQ GL + FL W P Sbjct: 182 GRDTMVGMQFHPEKSQDIGLRMIGNFLTWTP 212 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: 155 Number of extensions: 7 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: 212 Length adjustment: 21 Effective length of query: 192 Effective length of database: 191 Effective search space: 36672 Effective search space used: 36672 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 GFF916 PGA1_c09320 (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.9280.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-65 204.8 0.0 6.7e-65 204.6 0.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF916 PGA1_c09320 imidazole glycerol p Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF916 PGA1_c09320 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 204.6 0.0 6.7e-65 6.7e-65 2 197 .. 4 209 .. 3 210 .. 0.95 Alignments for each domain: == domain 1 score: 204.6 bits; conditional E-value: 6.7e-65 TIGR01855 2 vvidygvgNlksvkkalerv.....gaesevvkdskelekadklvlPGVGafkeamkklrele..lellaekvvkkk 71 ++idy++gNl+s +ka++r+ g e++v++d++ + +ad+lvlPG Gaf +++++lr ++ e+++e v++++ lcl|FitnessBrowser__Phaeo:GFF916 4 AIIDYESGNLHSAEKAFQRMarevdGGEVMVTSDADVVARADRLVLPGDGAFPACAEELRGHRgiYEAMVEAVEQNG 80 79***************998333334567899****************************9887889999******* PP TIGR01855 72 kpvlgiClGmQllfekseEgkevkglglikgkvkkleaek...kvPhiGWnevevvkesellkgleeearvYfvHsY 145 +p+lgiC+GmQl++ +++E ++++glg+++g+v+k++ + kvPh+GWn++ + ++++++ g++++++ YfvHsY lcl|FitnessBrowser__Phaeo:GFF916 81 RPFLGICVGMQLMATTGHEYRDTPGLGWVQGDVVKITPSDsalKVPHMGWNNLVIDHDHTIFDGITSGDHCYFVHSY 157 ************************************9888899********************************** PP TIGR01855 146 aveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 + ++++ + la +dyg++ +a++ +d++vg+QFHPEkS+++Gl+++ nfl lcl|FitnessBrowser__Phaeo:GFF916 158 HFRVNDPAERLAHVDYGSDVTAVIGRDTMVGMQFHPEKSQDIGLRMIGNFLT 209 *************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (212 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: 7.11 // [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