Align IGP synthase cyclase subunit; EC 4.1.3.- (characterized)
to candidate 6937806 Sama_1947 imidazole glycerol phosphate synthase subunit HisF (RefSeq)
Query= CharProtDB::CH_024847 (258 letters) >FitnessBrowser__SB2B:6937806 Length = 259 Score = 398 bits (1022), Expect = e-116 Identities = 192/257 (74%), Positives = 224/257 (87%) Query: 1 MLAKRIIPCLDVRDGQVVKGVQFRNHEIIGDIVPLAKRYAEEGADELVFYDITASSDGRV 60 MLAKRI+PCLDV+DG+VVKGVQFRNHEI+GDIVPLA RYA+EGADELVFYDI+AS+ G + Sbjct: 1 MLAKRIVPCLDVKDGKVVKGVQFRNHEIVGDIVPLAARYAQEGADELVFYDISASAKGAI 60 Query: 61 VDKSWVSRVAEVIDIPFCVAGGIKSLEDAAKILSFGADKISINSPALADPTLITRLADRF 120 VDKSWVSR+AE IDIPFCVAGGIK+ E A +IL+FGADKISINSPAL+DP+LI RL D F Sbjct: 61 VDKSWVSRIAERIDIPFCVAGGIKTAEQAREILAFGADKISINSPALSDPSLIRRLHDEF 120 Query: 121 GVQCIVVGIDTWYDAETGKYHVNQYTGDESRTRVTQWETLDWVQEVQKRGAGEIVLNMMN 180 G QC+VVGID++YDA +G Y V Q+TGDE+ T+ T+W TLDWV+EVQ++G GEIVLN+MN Sbjct: 121 GRQCVVVGIDSFYDAGSGNYTVKQFTGDEAATKDTRWHTLDWVEEVQRQGCGEIVLNVMN 180 Query: 181 QDGVRNGYDLEQLKKVREVCHVPLIASGGAGTMEHFLEAFRDADVDGALAASVFHKQIIN 240 QDGVR GYD+EQL KVR +C VPLIASGGAGTM HF E F DA VD ALAASVFHK IIN Sbjct: 181 QDGVRQGYDIEQLLKVRAICDVPLIASGGAGTMAHFAEVFTDARVDAALAASVFHKGIIN 240 Query: 241 IGELKAYLATQGVEIRI 257 IGELK +L +QG+ IR+ Sbjct: 241 IGELKQFLVSQGIAIRL 257 Lambda K H 0.321 0.138 0.409 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: 316 Number of extensions: 9 Number of successful extensions: 3 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: 258 Length of database: 259 Length adjustment: 24 Effective length of query: 234 Effective length of database: 235 Effective search space: 54990 Effective search space used: 54990 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 6937806 Sama_1947 (imidazole glycerol phosphate synthase subunit HisF (RefSeq))
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.22184.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-107 343.7 1.7 3.2e-107 343.5 1.7 1.0 1 lcl|FitnessBrowser__SB2B:6937806 Sama_1947 imidazole glycerol pho Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6937806 Sama_1947 imidazole glycerol phosphate synthase subunit HisF (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 343.5 1.7 3.2e-107 3.2e-107 1 254 [] 1 256 [. 1 256 [. 0.99 Alignments for each domain: == domain 1 score: 343.5 bits; conditional E-value: 3.2e-107 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekvfiPl 77 mlakri+pCLdvkdg+vvkGvqf+n++ +Gd+v+la++y++eGadelvf+di+as+++ +++++v+r+ae+++iP+ lcl|FitnessBrowser__SB2B:6937806 1 MLAKRIVPCLDVKDGKVVKGVQFRNHEIVGDIVPLAARYAQEGADELVFYDISASAKGAIVDKSWVSRIAERIDIPF 77 8**************************************************************************** PP TIGR00735 78 tvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaeneeakyevtikgGres.. 152 +v+GGik+ e+++++l++Gadk+sin++a+ +p li++l d fG+q++vv+id+ ++a + ++y+v++ +G+e lcl|FitnessBrowser__SB2B:6937806 78 CVAGGIKTAEQAREILAFGADKISINSPALSDPSLIRRLHDEFGRQCVVVGIDSFYDAGS--GNYTVKQFTGDEAat 152 ******************************************************999976..99*********9877 PP TIGR00735 153 ..tdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehleeaflkgkadaaL 227 t +++++w++ev+++G Gei+l++m++dG+++Gyd+e+l kv+ +++P+iasgGaG++ h++e+f+++++daaL lcl|FitnessBrowser__SB2B:6937806 153 kdTRWHTLDWVEEVQRQGCGEIVLNVMNQDGVRQGYDIEQLLKVRAICDVPLIASGGAGTMAHFAEVFTDARVDAAL 229 7799************************************************************************* PP TIGR00735 228 aasvfhkreltieevkeylaergvkvr 254 aasvfhk++++i+e+k++l+++g+ +r lcl|FitnessBrowser__SB2B:6937806 230 AASVFHKGIINIGELKQFLVSQGIAIR 256 *************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (259 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: 7.70 // [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