Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_011869428.1 MMARC5_RS08630 imidazole glycerol phosphate synthase cyclase subunit
Query= BRENDA::Q5NMD6 (255 letters) >NCBI__GCF_000016125.1:WP_011869428.1 Length = 272 Score = 263 bits (673), Expect = 2e-75 Identities = 136/270 (50%), Positives = 183/270 (67%), Gaps = 21/270 (7%) Query: 3 LCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGRGT 62 L RIIPCLD+ +GRVVKG NF +L DAGDPVE +K+Y+ GADEL FLDI+AS E R Sbjct: 2 LTKRIIPCLDIKEGRVVKGTNFVELRDAGDPVELSKIYNEQGADELVFLDITASFEKRDI 61 Query: 63 MLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADRFG 122 ++DVV RTAE F+PLTVGGG++ V+D R +L AGADK+++N++AV PEL+ E ++ FG Sbjct: 62 IIDVVKRTAEQVFIPLTVGGGIKTVDDFRKILRAGADKISINTSAVKTPELIKEASEIFG 121 Query: 123 AQCVVAAIDARRN--------------------GDHW-EVYTHGGRRPTGINALDHALNL 161 QCVV A+D +RN G W EVY +GGR TGI+A++ A + Sbjct: 122 TQCVVVAMDVKRNYITDIQDENLKDKNVFETELGSCWFEVYIYGGREGTGIDAIEWAKKV 181 Query: 162 TRLGAGEILLTSMDKDGTRDGYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHAS 221 LGAGEILLTSMD DGT+DGYDL LT+ ++ + +P+IASGG GN H+V+ G A Sbjct: 182 ENLGAGEILLTSMDADGTKDGYDLVLTKSISKNTNLPIIASGGCGNSKHVVDAFKDGKAD 241 Query: 222 ALLAASIFHFGQYSLAEAHEALAKAGLTVR 251 A L ASI H+ + ++ + + + K ++VR Sbjct: 242 AALMASILHYRECTVNDLKKEIEKNNISVR 271 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: 212 Number of extensions: 9 Number of successful extensions: 4 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: 272 Length adjustment: 25 Effective length of query: 230 Effective length of database: 247 Effective search space: 56810 Effective search space used: 56810 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_011869428.1 MMARC5_RS08630 (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.25667.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-123 397.6 2.3 1.1e-123 397.4 2.3 1.0 1 lcl|NCBI__GCF_000016125.1:WP_011869428.1 MMARC5_RS08630 imidazole glycero Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016125.1:WP_011869428.1 MMARC5_RS08630 imidazole glycerol phosphate synthase cyclase subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 397.4 2.3 1.1e-123 1.1e-123 1 254 [] 1 271 [. 1 271 [. 0.99 Alignments for each domain: == domain 1 score: 397.4 bits; conditional E-value: 1.1e-123 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverv 69 ml+kriipCLd+k+grvvkG++f +lrdaGdpvel+k y+e+Gadelvflditas ekr+++++vv+r+ lcl|NCBI__GCF_000016125.1:WP_011869428.1 1 MLTKRIIPCLDIKEGRVVKGTNFVELRDAGDPVELSKIYNEQGADELVFLDITASFEKRDIIIDVVKRT 69 8******************************************************************** PP TIGR00735 70 aekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaene 138 ae+vfiPltvgGGik+++d++k+lraGadk+sint+avk+pelike++++fG+q++vva+d kr++ ++ lcl|NCBI__GCF_000016125.1:WP_011869428.1 70 AEQVFIPLTVGGGIKTVDDFRKILRAGADKISINTSAVKTPELIKEASEIFGTQCVVVAMDVKRNYITD 138 ******************************************************************998 PP TIGR00735 139 e.................akyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlel 190 +++ev+i+gGre t++d++ewak+ve+lGaGeilltsmd+dGtk+Gydl l lcl|NCBI__GCF_000016125.1:WP_011869428.1 139 IqdenlkdknvfetelgsCWFEVYIYGGREGTGIDAIEWAKKVENLGAGEILLTSMDADGTKDGYDLVL 207 7899***************************************************************** PP TIGR00735 191 lkkvkeavkiPviasgGaGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 +k+++++ ++P+iasgG+G+ +h+ +af +gkadaaL+as++h+re+t++++k+ +++++++vr lcl|NCBI__GCF_000016125.1:WP_011869428.1 208 TKSISKNTNLPIIASGGCGNSKHVVDAFKDGKADAALMASILHYRECTVNDLKKEIEKNNISVR 271 **************************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (272 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: 8.87 // [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