Align IGP synthase glutamine amidotransferase subunit; EC 2.4.2.- (characterized)
to candidate WP_057506751.1 ABB28_RS00545 imidazole glycerol phosphate synthase subunit HisH
Query= CharProtDB::CH_024511 (196 letters) >NCBI__GCF_001431535.1:WP_057506751.1 Length = 201 Score = 176 bits (446), Expect = 3e-49 Identities = 91/194 (46%), Positives = 127/194 (65%), Gaps = 1/194 (0%) Query: 3 VVILDTGCANLNSVKSAIARHGYEPKVSRDPDVVLLADKLFLPGVGTAQAAMDQVREREL 62 V ++D G ANL SV+ A+ R G + ++ RD D + A ++ LPGVG A AM ++ + L Sbjct: 4 VALIDAGGANLGSVRYALERLGAQVRLVRDADGLRDARRVILPGVGAAVPAMQRLHAQGL 63 Query: 63 FDLIKACTQPVLGICLGMQLLGRRSEESNGVDLLGIIDEDVPKMTDF-GLPLPHMGWNRV 121 F+ ++ P+LGICLGMQLL RSEE GV LG+I V K+ G+ +PHMGWNR+ Sbjct: 64 FEPLRQLEVPLLGICLGMQLLFERSEEGGGVATLGLIPGTVRKLVPATGIRVPHMGWNRL 123 Query: 122 YPQAGNRLFQGIEDGAYFYFVHSYAMPVNPWTIAQCNYGEPFTAAVQKDNFYGVQFHPER 181 P G+ L + I + A YFVHSYA P+N T+A C++G F+A V+ ++G Q+HPER Sbjct: 124 LPLRGSPLLRDIPERASAYFVHSYAAPLNAHTVAACDHGGLFSAVVEHGRYFGAQYHPER 183 Query: 182 SGAAGAKLLKNFLE 195 SG GA LL+NFL+ Sbjct: 184 SGDTGALLLRNFLQ 197 Lambda K H 0.322 0.140 0.432 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: 130 Number of extensions: 8 Number of successful extensions: 2 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: 196 Length of database: 201 Length adjustment: 20 Effective length of query: 176 Effective length of database: 181 Effective search space: 31856 Effective search space used: 31856 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 45 (21.9 bits)
Align candidate WP_057506751.1 ABB28_RS00545 (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.27281.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-67 213.5 0.0 1.5e-67 213.3 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057506751.1 ABB28_RS00545 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057506751.1 ABB28_RS00545 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 213.3 0.0 1.5e-67 1.5e-67 1 197 [. 4 197 .. 4 198 .. 0.98 Alignments for each domain: == domain 1 score: 213.3 bits; conditional E-value: 1.5e-67 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvk 69 +++id+g +Nl sv+ aler+ga++++v+d++ l++a +++lPGVGa+ am++l+ ++ l+ e +++ lcl|NCBI__GCF_001431535.1:WP_057506751.1 4 VALIDAGGANLGSVRYALERLGAQVRLVRDADGLRDARRVILPGVGAAVPAMQRLHAQG--LF-EPLRQ 69 689******************************************************99..66.999** PP TIGR01855 70 kkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek..kvPhiGWnevevvkesellkgleee 136 + p+lgiClGmQllfe+seEg+ v +lgli+g+v+kl ++ +vPh+GWn++ +++ s+ll+++ e lcl|NCBI__GCF_001431535.1:WP_057506751.1 70 LEVPLLGICLGMQLLFERSEEGGGVATLGLIPGTVRKLVPATgiRVPHMGWNRLLPLRGSPLLRDIPER 138 **************************************999889************************* PP TIGR01855 137 arvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 a++YfvHsYa++l+ +++a++d+g f a+ve+++++g+Q+HPE+Sg+tG+ ll+nfl+ lcl|NCBI__GCF_001431535.1:WP_057506751.1 139 ASAYFVHSYAAPLNA--HTVAACDHGGLFSAVVEHGRYFGAQYHPERSGDTGALLLRNFLQ 197 *************98..99****************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (201 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: 5.70 // [ok]
This GapMind analysis is from Apr 10 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