Align IGP synthase glutamine amidotransferase subunit; EC 2.4.2.- (characterized)
to candidate BWI76_RS18940 BWI76_RS18940 imidazole glycerol phosphate synthase subunit HisH
Query= CharProtDB::CH_024511 (196 letters) >FitnessBrowser__Koxy:BWI76_RS18940 Length = 196 Score = 358 bits (920), Expect = e-104 Identities = 172/196 (87%), Positives = 189/196 (96%) Query: 1 MNVVILDTGCANLNSVKSAIARHGYEPKVSRDPDVVLLADKLFLPGVGTAQAAMDQVRER 60 MNVVILDTGCANLNSVKSA++RHGYEP+VSRDPDVVL ADKLFLPGVGTAQAAMDQ+RER Sbjct: 1 MNVVILDTGCANLNSVKSAVSRHGYEPQVSRDPDVVLRADKLFLPGVGTAQAAMDQLRER 60 Query: 61 ELFDLIKACTQPVLGICLGMQLLGRRSEESNGVDLLGIIDEDVPKMTDFGLPLPHMGWNR 120 EL +LIKACTQPVLGICLGMQLLG+RSEE+NGVDLLGII++DVPKMTD GLPLPHMGWN+ Sbjct: 61 ELIELIKACTQPVLGICLGMQLLGKRSEENNGVDLLGIIEQDVPKMTDHGLPLPHMGWNQ 120 Query: 121 VYPQAGNRLFQGIEDGAYFYFVHSYAMPVNPWTIAQCNYGEPFTAAVQKDNFYGVQFHPE 180 VY +AG+RLF+GIEDGAYFYFVHSYAMPVN TIAQC+YGE FTAAVQKDNF+GVQFHPE Sbjct: 121 VYAKAGDRLFRGIEDGAYFYFVHSYAMPVNVNTIAQCSYGEAFTAAVQKDNFFGVQFHPE 180 Query: 181 RSGAAGAKLLKNFLEM 196 RSG+AGA+LLKNFLEM Sbjct: 181 RSGSAGAQLLKNFLEM 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: 230 Number of extensions: 1 Number of successful extensions: 1 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 BWI76_RS18940 BWI76_RS18940 (imidazole glycerol phosphate synthase subunit HisH)
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.28492.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-78 248.4 0.0 2.9e-78 248.3 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS18940 BWI76_RS18940 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS18940 BWI76_RS18940 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 248.3 0.0 2.9e-78 2.9e-78 1 198 [] 3 196 .] 3 196 .] 0.98 Alignments for each domain: == domain 1 score: 248.3 bits; conditional E-value: 2.9e-78 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkk 71 +v++d+g++Nl+svk+a+ r+g+e++v++d + + +adkl+lPGVG++++am++lre+e l+ e +++++ lcl|FitnessBrowser__Koxy:BWI76_RS18940 3 VVILDTGCANLNSVKSAVSRHGYEPQVSRDPDVVLRADKLFLPGVGTAQAAMDQLRERE--LI-ELIKACT 70 79*******************************************************88..44.889**** PP TIGR01855 72 kpvlgiClGmQllfekseEgkevkglglikgkvkkleaek.kvPhiGWnevevvkesellkgleeearvYf 141 +pvlgiClGmQll ++seE++ v+ lg+i+++v k++++ ++Ph+GWn+v ++ ++l++g+e++a++Yf lcl|FitnessBrowser__Koxy:BWI76_RS18940 71 QPVLGICLGMQLLGKRSEENNGVDLLGIIEQDVPKMTDHGlPLPHMGWNQVYAKAGDRLFRGIEDGAYFYF 141 *************************************9989****************************** PP TIGR01855 142 vHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknflel 198 vHsYa++++ +++a++ yge f+aav+kdn++gvQFHPE+Sg++G++llknfle+ lcl|FitnessBrowser__Koxy:BWI76_RS18940 142 VHSYAMPVNV--NTIAQCSYGEAFTAAVQKDNFFGVQFHPERSGSAGAQLLKNFLEM 196 *********8..89****************************************986 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.20 // [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