Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_093428506.1 BM272_RS09260 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q5NMD6 (255 letters) >NCBI__GCF_900112605.1:WP_093428506.1 Length = 253 Score = 330 bits (847), Expect = 1e-95 Identities = 166/252 (65%), Positives = 198/252 (78%), Gaps = 1/252 (0%) Query: 1 MTLCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGR 60 M+L RIIPCLDV GRVVKGV F D+ DAGDPVE A+ YD GADEL FLDI+ASHEGR Sbjct: 1 MSLAKRIIPCLDVEGGRVVKGVQFVDIRDAGDPVEAAQRYDQQGADELTFLDITASHEGR 60 Query: 61 GTMLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADR 120 GT+L+VV A F+PLTVGGGVR VED RALL AGADKVA+N+AAV P LV ADR Sbjct: 61 GTILEVVEAVAGRVFIPLTVGGGVRAVEDVRALLAAGADKVAINTAAVNDPALVRAAADR 120 Query: 121 FGAQCVVAAIDARR-NGDHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMDKDGT 179 FG QC+V AIDAR+ WE++THGGR PTG++A++ A + GAGE+L+TSMD+DGT Sbjct: 121 FGRQCIVVAIDARQVEPGRWEIFTHGGRTPTGLDAVEWAARMEEEGAGELLVTSMDRDGT 180 Query: 180 RDGYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYSLAEA 239 RDG+D++LTR +AD V VPVIASGGVGNLDH+ EG+ GHA A+LAASIFHFG+Y++ EA Sbjct: 181 RDGFDIDLTRAIADRVGVPVIASGGVGNLDHLAEGLRDGHADAVLAASIFHFGEYTIGEA 240 Query: 240 HEALAKAGLTVR 251 L +AGL VR Sbjct: 241 KAHLHRAGLPVR 252 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: 275 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: 255 Length of database: 253 Length adjustment: 24 Effective length of query: 231 Effective length of database: 229 Effective search space: 52899 Effective search space used: 52899 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_093428506.1 BM272_RS09260 (imidazole glycerol phosphate synthase subunit HisF)
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.3454219.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-114 367.0 1.1 2.4e-114 366.9 1.1 1.0 1 NCBI__GCF_900112605.1:WP_093428506.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900112605.1:WP_093428506.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 366.9 1.1 2.4e-114 2.4e-114 2 254 .] 3 252 .. 2 252 .. 0.99 Alignments for each domain: == domain 1 score: 366.9 bits; conditional E-value: 2.4e-114 TIGR00735 2 lakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekvf 74 lakriipCLdv+ grvvkGvqf ++rdaGdpve a++yd++Gadel+flditas+e+r t+levve va +vf NCBI__GCF_900112605.1:WP_093428506.1 3 LAKRIIPCLDVEGGRVVKGVQFVDIRDAGDPVEAAQRYDQQGADELTFLDITASHEGRGTILEVVEAVAGRVF 75 9************************************************************************ PP TIGR00735 75 iPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaeneeakyevtik 147 iPltvgGG++ +edv+ ll+aGadkv+intaav++p l++ +adrfG+q+ivvaida++++ + +e+ ++ NCBI__GCF_900112605.1:WP_093428506.1 76 IPLTVGGGVRAVEDVRALLAAGADKVAINTAAVNDPALVRAAADRFGRQCIVVAIDARQVEP---GRWEIFTH 145 *********************************************************99876...69****** PP TIGR00735 148 gGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehleeaflk 220 gGr+ t+ld+vewa+++ee GaGe+l+tsmd+dGt++G+d+ l+++++++v +PviasgG+G+ +hl+e++ + NCBI__GCF_900112605.1:WP_093428506.1 146 GGRTPTGLDAVEWAARMEEEGAGELLVTSMDRDGTRDGFDIDLTRAIADRVGVPVIASGGVGNLDHLAEGLRD 218 ************************************************************************* PP TIGR00735 221 gkadaaLaasvfhkreltieevkeylaergvkvr 254 g+ada+Laas+fh++e+ti+e k++l+ g++vr NCBI__GCF_900112605.1:WP_093428506.1 219 GHADAVLAASIFHFGEYTIGEAKAHLHRAGLPVR 252 ********************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (253 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: 19.89 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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