Align IGP synthase glutamine amidotransferase subunit; EC 2.4.2.- (characterized)
to candidate 6937804 Sama_1945 imidazole glycerol phosphate synthase subunit HisH (RefSeq)
Query= CharProtDB::CH_024511 (196 letters) >FitnessBrowser__SB2B:6937804 Length = 237 Score = 200 bits (508), Expect = 2e-56 Identities = 106/196 (54%), Positives = 132/196 (67%), Gaps = 5/196 (2%) Query: 3 VVILDTGCANLNSVKSAIARHGYEPKVSRDPDVVLLADKLFLPGVGTAQAAMDQVREREL 62 +VI+DTGCANL+SVK A R G + VS D +V+ A +L LPGVGTA AAMD +R R L Sbjct: 18 LVIIDTGCANLSSVKFAFERLGAKVLVSPDSEVLRAAPRLVLPGVGTAAAAMDALRARAL 77 Query: 63 FDLIKACTQPVLGICLGMQLLGRRSEE----SNGVDLLGIIDEDVPKMTDFGLPLPHMGW 118 LI QPVLG+CLGMQLL RS E +D L II ++ ++ G PLPHMGW Sbjct: 78 DKLIPTLRQPVLGVCLGMQLLMTRSHERGAKGEDIDCLDIIPGEIRELDASGHPLPHMGW 137 Query: 119 NRVYPQAGNRLFQGIEDGAYFYFVHSYAMPVNPWTIAQCNYGEPFTAAVQKDNFYGVQFH 178 N++ + + LF GIE G + YFVHS+ P + TIA C YGE F+AA+ KDNF GVQFH Sbjct: 138 NQL-TVSNHPLFAGIEPGEWVYFVHSFCAPTSAATIASCEYGETFSAAIAKDNFMGVQFH 196 Query: 179 PERSGAAGAKLLKNFL 194 PE+S GAK+L+NFL Sbjct: 197 PEKSATTGAKILRNFL 212 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: 147 Number of extensions: 4 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: 237 Length adjustment: 22 Effective length of query: 174 Effective length of database: 215 Effective search space: 37410 Effective search space used: 37410 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 6937804 Sama_1945 (imidazole glycerol phosphate synthase subunit HisH (RefSeq))
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.11496.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-65 206.3 0.0 2.4e-65 206.1 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6937804 Sama_1945 imidazole glycerol pho Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6937804 Sama_1945 imidazole glycerol phosphate synthase subunit HisH (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 206.1 0.0 2.4e-65 2.4e-65 2 197 .. 19 213 .. 18 214 .. 0.94 Alignments for each domain: == domain 1 score: 206.1 bits; conditional E-value: 2.4e-65 TIGR01855 2 vvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkpvlgiC 78 v+id+g++Nl+svk a+er+ga++ v+ ds+ l+ a +lvlPGVG++++am+ lr + l++l + + ++pvlg+C lcl|FitnessBrowser__SB2B:6937804 19 VIIDTGCANLSSVKFAFERLGAKVLVSPDSEVLRAAPRLVLPGVGTAAAAMDALRARALDKL---IPTLRQPVLGVC 92 8*******************************************************885555...889999****** PP TIGR01855 79 lGmQllfekseE....gkevkglglikgkvkkleaek.kvPhiGWnevevvkesellkgleeearvYfvHsYavele 150 lGmQll+ +s+E g++ ++l +i+g+++ l+a+ ++Ph+GWn+++ v++++l++g+e ++ vYfvHs+ ++++ lcl|FitnessBrowser__SB2B:6937804 93 LGMQLLMTRSHErgakGEDIDCLDIIPGEIRELDASGhPLPHMGWNQLT-VSNHPLFAGIEPGEWVYFVHSFCAPTS 168 ***********9654445679*************9988********986.57889********************99 PP TIGR01855 151 eeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 a++a+++yge+f aa++kdn++gvQFHPEkS++tG+k+l+nfl+ lcl|FitnessBrowser__SB2B:6937804 169 A--ATIASCEYGETFSAAIAKDNFMGVQFHPEKSATTGAKILRNFLA 213 7..9*****************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (237 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: 5.89 // [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