Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate AZOBR_RS01685 AZOBR_RS01685 imidazole glycerol phosphate synthase
Query= BRENDA::Q5NMD6 (255 letters) >FitnessBrowser__azobra:AZOBR_RS01685 Length = 265 Score = 342 bits (876), Expect = 6e-99 Identities = 168/247 (68%), Positives = 203/247 (82%), Gaps = 1/247 (0%) Query: 6 RIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGRGTMLD 65 R+IPCLDV DGRVVKGVNF DL+DAGDPVEQA+VYD GADEL FLDI+ASHE R T+ D Sbjct: 5 RVIPCLDVKDGRVVKGVNFVDLIDAGDPVEQARVYDREGADELTFLDITASHENRDTIYD 64 Query: 66 VVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADRFGAQC 125 VV RTAE FMPLTVGGGVR VED R LLLAGADKV++N+AA+ RPE V E A++FGAQC Sbjct: 65 VVRRTAEQVFMPLTVGGGVRTVEDIRKLLLAGADKVSINTAAIHRPEFVQEAAEKFGAQC 124 Query: 126 VVAAIDARR-NGDHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMDKDGTRDGYD 184 +V AIDA++ WE++THGGR+ TGI+A++ A + GAGEILLTSMD+DGT+ G+D Sbjct: 125 IVVAIDAKQVEPGRWEIFTHGGRKATGIDAIEWAKRMESYGAGEILLTSMDRDGTKSGFD 184 Query: 185 LELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYSLAEAHEALA 244 L LTR VAD + +PVIASGGVG LDH+VEG+ +GHA+A+LAASIFHFG Y++ +A ALA Sbjct: 185 LALTRKVADGLRIPVIASGGVGTLDHLVEGIREGHATAVLAASIFHFGTYTIGQAKAALA 244 Query: 245 KAGLTVR 251 AG+ VR Sbjct: 245 DAGIPVR 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: 273 Number of extensions: 10 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: 265 Length adjustment: 24 Effective length of query: 231 Effective length of database: 241 Effective search space: 55671 Effective search space used: 55671 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 AZOBR_RS01685 AZOBR_RS01685 (imidazole glycerol phosphate synthase)
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.31737.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.7e-115 368.7 1.3 7.5e-115 368.5 1.3 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS01685 AZOBR_RS01685 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS01685 AZOBR_RS01685 imidazole glycerol phosphate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 368.5 1.3 7.5e-115 7.5e-115 1 254 [] 1 251 [. 1 251 [. 0.99 Alignments for each domain: == domain 1 score: 368.5 bits; conditional E-value: 7.5e-115 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverv 69 ml r+ipCLdvkdgrvvkGv+f +l daGdpve a++yd+eGadel+flditas+e+r+t+ +vv+r+ lcl|FitnessBrowser__azobra:AZOBR_RS01685 1 MLKMRVIPCLDVKDGRVVKGVNFVDLIDAGDPVEQARVYDREGADELTFLDITASHENRDTIYDVVRRT 69 7899***************************************************************** PP TIGR00735 70 aekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaene 138 ae+vf+PltvgGG++++ed++kll aGadkvsintaa+++pe+++e+a++fG+q+ivvaidak+++ lcl|FitnessBrowser__azobra:AZOBR_RS01685 70 AEQVFMPLTVGGGVRTVEDIRKLLLAGADKVSINTAAIHRPEFVQEAAEKFGAQCIVVAIDAKQVEP-- 136 ***************************************************************9876.. PP TIGR00735 139 eakyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgG 207 + +e+ ++gGr+ t++d++ewak++e+ GaGeilltsmd+dGtksG+dl+l++kv++ ++iPviasgG lcl|FitnessBrowser__azobra:AZOBR_RS01685 137 -GRWEIFTHGGRKATGIDAIEWAKRMESYGAGEILLTSMDRDGTKSGFDLALTRKVADGLRIPVIASGG 204 .69****************************************************************** PP TIGR00735 208 aGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 +G+ +hl e++ +g+a a+Laas+fh++ +ti++ k+ la+ g++vr lcl|FitnessBrowser__azobra:AZOBR_RS01685 205 VGTLDHLVEGIREGHATAVLAASIFHFGTYTIGQAKAALADAGIPVR 251 *********************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (265 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: 8.82 // [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