Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_011386875.1 AMB_RS22925 imidazole glycerol phosphate synthase cyclase subunit
Query= BRENDA::Q5NMD6 (255 letters) >NCBI__GCF_000009985.1:WP_011386875.1 Length = 252 Score = 341 bits (875), Expect = 7e-99 Identities = 169/247 (68%), Positives = 205/247 (82%), Gaps = 1/247 (0%) Query: 6 RIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGRGTMLD 65 RIIPCLDV DGRVVKGVNF DL+DAGDPVEQAK+YD AGADEL FLDI+ASHE R T+ D Sbjct: 5 RIIPCLDVKDGRVVKGVNFVDLIDAGDPVEQAKLYDKAGADELTFLDITASHENRDTIYD 64 Query: 66 VVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADRFGAQC 125 VV RTAE CFMPLTVGGGVR +D R LLLAGADKV++N+AAV RPE V E A++FG+QC Sbjct: 65 VVRRTAEQCFMPLTVGGGVRVNDDIRKLLLAGADKVSINTAAVHRPEFVREAAEKFGSQC 124 Query: 126 VVAAIDARRNG-DHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMDKDGTRDGYD 184 +V AIDA++ G +E++THGGR TGI+A++ A +T GAGEILLTSMD+DGT+ G++ Sbjct: 125 IVVAIDAKQTGPGKFEIFTHGGRNATGIDAVEWARRMTEYGAGEILLTSMDRDGTKQGFN 184 Query: 185 LELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYSLAEAHEALA 244 + LTR VAD+V VPVIASGGVGNLDH+VEG+ GHA+A+LAASIFHFG Y++A+A + Sbjct: 185 IPLTRAVADAVTVPVIASGGVGNLDHLVEGIRDGHATAVLAASIFHFGTYTIAQAKAHMR 244 Query: 245 KAGLTVR 251 AG+ VR Sbjct: 245 AAGIPVR 251 Lambda K H 0.320 0.136 0.400 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: 271 Number of extensions: 6 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: 255 Length of database: 252 Length adjustment: 24 Effective length of query: 231 Effective length of database: 228 Effective search space: 52668 Effective search space used: 52668 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 (21.8 bits) S2: 47 (22.7 bits)
Align candidate WP_011386875.1 AMB_RS22925 (imidazole glycerol phosphate synthase cyclase subunit)
to HMM TIGR00735 (hisF: imidazoleglycerol phosphate synthase, cyclase subunit)
# 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/TIGR00735.hmm # target sequence database: /tmp/gapView.20184.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00735 [M=254] Accession: TIGR00735 Description: hisF: imidazoleglycerol phosphate synthase, cyclase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-110 354.8 1.3 1.3e-110 354.6 1.3 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011386875.1 AMB_RS22925 imidazole glycerol p Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011386875.1 AMB_RS22925 imidazole glycerol phosphate synthase cyclase subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 354.6 1.3 1.3e-110 1.3e-110 1 254 [] 1 251 [. 1 251 [. 0.99 Alignments for each domain: == domain 1 score: 354.6 bits; conditional E-value: 1.3e-110 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverv 69 ml riipCLdvkdgrvvkGv+f +l daGdpve ak yd+ Gadel+flditas+e+r+t+ +vv+r+ lcl|NCBI__GCF_000009985.1:WP_011386875.1 1 MLKMRIIPCLDVKDGRVVKGVNFVDLIDAGDPVEQAKLYDKAGADELTFLDITASHENRDTIYDVVRRT 69 7899***************************************************************** PP TIGR00735 70 aekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaene 138 ae+ f+PltvgGG++ +d++kll aGadkvsintaav++pe+++e+a++fGsq+ivvaidak++ lcl|NCBI__GCF_000009985.1:WP_011386875.1 70 AEQCFMPLTVGGGVRVNDDIRKLLLAGADKVSINTAAVHRPEFVREAAEKFGSQCIVVAIDAKQTGP-- 136 ***************************************************************9886.. PP TIGR00735 139 eakyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgG 207 +k+e+ ++gGr+ t++d+vewa++++e GaGeilltsmd+dGtk+G+++ l+++v++av++PviasgG lcl|NCBI__GCF_000009985.1:WP_011386875.1 137 -GKFEIFTHGGRNATGIDAVEWARRMTEYGAGEILLTSMDRDGTKQGFNIPLTRAVADAVTVPVIASGG 204 .69****************************************************************** PP TIGR00735 208 aGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 +G+ +hl e++ +g+a a+Laas+fh++ +ti + k+++++ g++vr lcl|NCBI__GCF_000009985.1:WP_011386875.1 205 VGNLDHLVEGIRDGHATAVLAASIFHFGTYTIAQAKAHMRAAGIPVR 251 *********************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (252 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.93 // [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