Align imidazole glycerol-phosphate synthase (subunit 1/2) (EC 4.3.2.10) (characterized)
to candidate WP_083763585.1 AMB_RS22935 imidazole glycerol phosphate synthase subunit HisH
Query= BRENDA::Q5NMD4 (213 letters) >NCBI__GCF_000009985.1:WP_083763585.1 Length = 216 Score = 221 bits (564), Expect = 6e-63 Identities = 115/212 (54%), Positives = 140/212 (66%), Gaps = 7/212 (3%) Query: 9 VALIDYGAGNLRSVANA---LLASGLARENLVVTANPDEVLQADRVVLPGVGAFASCMQA 65 VA+IDYG+GNLRS A A ++A ++ VT +P V +ADRVVLPGVGAFA C Sbjct: 5 VAIIDYGSGNLRSAAKAFERVVAEASLNLSVAVTNDPKVVDRADRVVLPGVGAFADCRAG 64 Query: 66 LKAIPDMVPALEKAVLEKGRPFLGICVGMQLLADQGEEYGVHQGLGWIKGKVTPLRPNDP 125 L A+P M L + VL +G PF GICVGMQL+A G E+G+H GLGW+ G+V PL D Sbjct: 65 LLALPGMAETLTERVLARGVPFFGICVGMQLMASIGREHGLHAGLGWVAGEVVPLGVEDQ 124 Query: 126 SCKVPHMGWNQIGLTTDSHPLLRA----GEAYFLHSYAFVPEDESTLLATTEHGGLVTAA 181 KVPHMGWNQ+ SHPLL AYF+HSY F P + + LA E+GG VTA Sbjct: 125 GLKVPHMGWNQLVPDGLSHPLLAGLDSEAHAYFVHSYKFEPANPAHRLAHVEYGGQVTAV 184 Query: 182 VGRDNIMGVQFHPEKSQSYGLEFLSRFLDWNP 213 VGRDN++G QFHPEKSQ GL+ +S FL W P Sbjct: 185 VGRDNMVGTQFHPEKSQITGLKVISNFLTWTP 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: 197 Number of extensions: 12 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 WP_083763585.1 AMB_RS22935 (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.28951.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-62 196.8 0.0 2e-62 196.6 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_083763585.1 AMB_RS22935 imidazole glycerol p Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_083763585.1 AMB_RS22935 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 196.6 0.0 2e-62 2e-62 1 197 [. 5 213 .. 5 214 .. 0.92 Alignments for each domain: == domain 1 score: 196.6 bits; conditional E-value: 2e-62 TIGR01855 1 ivvidygvgNlksvkkalervgae......sevvkdskelekadklvlPGVGafkeamkklrele..le 61 +++idyg+gNl+s +ka+erv ae + v++d k +++ad++vlPGVGaf+++ + l l e lcl|NCBI__GCF_000009985.1:WP_083763585.1 5 VAIIDYGSGNLRSAAKAFERVVAEaslnlsVAVTNDPKVVDRADRVVLPGVGAFADCRAGLLALPgmAE 73 79*****************986652222216789999**********************9998866788 PP TIGR01855 62 llaekvvkkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek...kvPhiGWnevevv.ke 126 +l+e+v +++ p+ giC+GmQl+++ + E++ + glg++ g+v+ l e kvPh+GWn++ + + lcl|NCBI__GCF_000009985.1:WP_083763585.1 74 TLTERVLARGVPFFGICVGMQLMASIGREHGLHAGLGWVAGEVVPLGVEDqglKVPHMGWNQLVPDgLS 142 999******************************************98877789*********9886257 PP TIGR01855 127 sellkgleeearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknf 195 ++ll+gl++ea++YfvHsY+ e+++ + la ++yg + +a+v +dn+vg+QFHPEkS+ tGlk+++nf lcl|NCBI__GCF_000009985.1:WP_083763585.1 143 HPLLAGLDSEAHAYFVHSYKFEPANPAHRLAHVEYGGQVTAVVGRDNMVGTQFHPEKSQITGLKVISNF 211 7******************************************************************** PP TIGR01855 196 le 197 l lcl|NCBI__GCF_000009985.1:WP_083763585.1 212 LT 213 86 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 5.43 // [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