Align IGP synthase glutamine amidotransferase subunit; EC 2.4.2.- (characterized)
to candidate 350908 BT1380 imidazole glycerol phosphate synthase subunit hisH (NCBI ptt file)
Query= CharProtDB::CH_024511 (196 letters) >FitnessBrowser__Btheta:350908 Length = 196 Score = 164 bits (414), Expect = 1e-45 Identities = 85/198 (42%), Positives = 122/198 (61%), Gaps = 4/198 (2%) Query: 1 MNVVILDTGCANLNSVKSAIARHGYEPKVSRDPDVVLLADKLFLPGVGTAQAAMDQVRER 60 M V ++ N+ SV A+ R G E ++ D +++ ADK+ PGVG A M+ ++ Sbjct: 1 MKVAVVKYNAGNIRSVDYALKRLGVEAVITADKEILQSADKVIFPGVGEAGTTMNHLKAT 60 Query: 61 ELFDLIKACTQPVLGICLGMQLLGRRSEESNGVDLLGIIDEDVPKMTD--FGLPLPHMGW 118 L +LIK QPV GICLGMQL+ R SEE VD L I D DV + +PHMGW Sbjct: 61 GLDELIKNLRQPVFGICLGMQLMCRHSEEGE-VDCLNIFDVDVKRFVPQKHEDKVPHMGW 119 Query: 119 NRVYPQAGNRLFQGIEDGAYFYFVHSYAMPVNPWTIAQCNYGEPFTAAVQKDNFYGVQFH 178 N + + ++LF+G + + YFVHS+ +PV +T A+ +Y PF+AA+ KDNFY QFH Sbjct: 120 NTI-GKTNSKLFEGFTEEEFVYFVHSFYVPVCDFTAAETDYIHPFSAALHKDNFYATQFH 178 Query: 179 PERSGAAGAKLLKNFLEM 196 PE+SG G ++L+NFL++ Sbjct: 179 PEKSGKTGERVLRNFLDL 196 Lambda K H 0.322 0.140 0.432 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: 134 Number of extensions: 3 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: 196 Length of database: 196 Length adjustment: 20 Effective length of query: 176 Effective length of database: 176 Effective search space: 30976 Effective search space used: 30976 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: 45 (21.9 bits)
Align candidate 350908 BT1380 (imidazole glycerol phosphate synthase subunit hisH (NCBI ptt file))
to HMM TIGR01855 (hisH: imidazole glycerol phosphate synthase, glutamine amidotransferase subunit (EC 2.4.2.-))
# 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/TIGR01855.hmm # target sequence database: /tmp/gapView.9904.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01855 [M=198] Accession: TIGR01855 Description: IMP_synth_hisH: imidazole glycerol phosphate synthase, glutamine amidotransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-66 209.9 0.0 1.9e-66 209.7 0.0 1.0 1 lcl|FitnessBrowser__Btheta:350908 BT1380 imidazole glycerol phosph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:350908 BT1380 imidazole glycerol phosphate synthase subunit hisH (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 209.7 0.0 1.9e-66 1.9e-66 1 197 [. 3 195 .. 3 196 .] 0.95 Alignments for each domain: == domain 1 score: 209.7 bits; conditional E-value: 1.9e-66 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkpvlg 76 ++v+ y++gN++sv al+r+g+e+++++d++ l++adk+++PGVG++ +m++l+ ++l+ +++ ++pv g lcl|FitnessBrowser__Btheta:350908 3 VAVVKYNAGNIRSVDYALKRLGVEAVITADKEILQSADKVIFPGVGEAGTTMNHLKATGLDE---LIKNLRQPVFG 75 78*******************************************************99555...589999***** PP TIGR01855 77 iClGmQllfekseEgkevkglglikgkvkkleaek...kvPhiGWnevevvkesellkgleeearvYfvHsYavel 149 iClGmQl+ ++seEg ev++l +++ +vk++ +k kvPh+GWn++ +++s+l++g +ee+ vYfvHs++v++ lcl|FitnessBrowser__Btheta:350908 76 ICLGMQLMCRHSEEG-EVDCLNIFDVDVKRFVPQKhedKVPHMGWNTI-GKTNSKLFEGFTEEEFVYFVHSFYVPV 149 **************6.79*************8777788********66.566788********************* PP TIGR01855 150 eeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 + + a +dy + f aa++kdn++++QFHPEkSgktG ++l+nfl+ lcl|FitnessBrowser__Btheta:350908 150 CD--FTAAETDYIHPFSAALHKDNFYATQFHPEKSGKTGERVLRNFLD 195 97..9*****************************************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (196 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: 6.03 // [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