Align Imidazole glycerol phosphate synthase subunit HisF; IGP synthase cyclase subunit; IGP synthase subunit HisF; ImGP synthase subunit HisF; IGPS subunit HisF; EC 4.3.2.10 (characterized)
to candidate WP_012402123.1 BPHY_RS14000 imidazole glycerol phosphate synthase cyclase subunit
Query= SwissProt::Q7SIB9 (252 letters) >NCBI__GCF_000020045.1:WP_012402123.1 Length = 257 Score = 307 bits (787), Expect = 1e-88 Identities = 157/257 (61%), Positives = 201/257 (78%), Gaps = 6/257 (2%) Query: 1 MSLAKRIVPCLDVHAGRVVKGVNFVNLRDAGDPVEAARAYDEAGADELVFLDISATHEER 60 M+LAKRI+PCLDV AGRVVKGVNFV LRDAGDPVE AR YDE GADEL FLDI+AT ++R Sbjct: 1 MALAKRIIPCLDVTAGRVVKGVNFVELRDAGDPVEIARRYDEQGADELTFLDITATSDQR 60 Query: 61 AILLDVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELADH 120 ++L ++ VA +VFIPLTVGGGVR++ED R+LL +GADKVS+NS+AV P+L+R+ D Sbjct: 61 DLILPIIEAVASQVFIPLTVGGGVRAVEDVRRLLNAGADKVSMNSSAVANPQLVRDSTDK 120 Query: 121 FGAQAVVLAIDAR---WRGDFP--EVHVAGGRVPTGLHAVEWAVKGVELGAGEILLTSMD 175 +G+Q +V+AIDA+ G+ P EV GGR TGL AVEWA + ELGAGEILLTSMD Sbjct: 121 YGSQCIVVAIDAKRVSAEGETPRWEVFTHGGRKNTGLDAVEWARRMAELGAGEILLTSMD 180 Query: 176 RDGTKEGYDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAFQAG-AEAALAASVFHFGEIP 234 RDGTK G+D+ LTR V++AV +PVIASGG G ++H + G A+A LAAS+FH+GE Sbjct: 181 RDGTKSGFDIALTRAVSDAVSIPVIASGGVGSLQHLADGITQGRADAVLAASIFHYGEHT 240 Query: 235 IPKLKRYLAEKGVHVRL 251 + + KR++A++G+ VRL Sbjct: 241 VGECKRFMADQGISVRL 257 Lambda K H 0.321 0.138 0.398 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: 240 Number of extensions: 13 Number of successful extensions: 5 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: 252 Length of database: 257 Length adjustment: 24 Effective length of query: 228 Effective length of database: 233 Effective search space: 53124 Effective search space used: 53124 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: 47 (22.7 bits)
Align candidate WP_012402123.1 BPHY_RS14000 (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.22000.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-119 383.6 0.9 2.2e-119 383.4 0.9 1.0 1 lcl|NCBI__GCF_000020045.1:WP_012402123.1 BPHY_RS14000 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020045.1:WP_012402123.1 BPHY_RS14000 imidazole glycerol phosphate synthase cyclase subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 383.4 0.9 2.2e-119 2.2e-119 2 254 .] 3 256 .. 2 256 .. 0.98 Alignments for each domain: == domain 1 score: 383.4 bits; conditional E-value: 2.2e-119 TIGR00735 2 lakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverva 70 lakriipCLdv++grvvkGv+f +lrdaGdpve+a++yde+Gadel+fldita+s++r+ +l ++e va lcl|NCBI__GCF_000020045.1:WP_012402123.1 3 LAKRIIPCLDVTAGRVVKGVNFVELRDAGDPVEIARRYDEQGADELTFLDITATSDQRDLILPIIEAVA 71 9******************************************************************** PP TIGR00735 71 ekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakrea.ene 138 +vfiPltvgGG++ +edv++ll+aGadkvs+n++av++p+l+++ +d++Gsq+ivvaidakr+ e e lcl|NCBI__GCF_000020045.1:WP_012402123.1 72 SQVFIPLTVGGGVRAVEDVRRLLNAGADKVSMNSSAVANPQLVRDSTDKYGSQCIVVAIDAKRVSaEGE 140 **************************************************************9861556 PP TIGR00735 139 eakyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgG 207 +ev ++gGr++t+ld+vewa++++elGaGeilltsmd+dGtksG+d++l+++v++av+iPviasgG lcl|NCBI__GCF_000020045.1:WP_012402123.1 141 TPRWEVFTHGGRKNTGLDAVEWARRMAELGAGEILLTSMDRDGTKSGFDIALTRAVSDAVSIPVIASGG 209 79******************************************************************* PP TIGR00735 208 aGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 +G+ +hl++++++g+ada+Laas+fh++e t++e k+++a++g++vr lcl|NCBI__GCF_000020045.1:WP_012402123.1 210 VGSLQHLADGITQGRADAVLAASIFHYGEHTVGECKRFMADQGISVR 256 *********************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (257 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: 7.07 // [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