Align IGP synthase glutamine amidotransferase subunit; EC 2.4.2.- (characterized)
to candidate 5209748 Shew_2201 imidazole glycerol phosphate synthase subunit HisH (RefSeq)
Query= CharProtDB::CH_024511 (196 letters) >FitnessBrowser__PV4:5209748 Length = 224 Score = 211 bits (537), Expect = 8e-60 Identities = 102/204 (50%), Positives = 145/204 (71%), Gaps = 10/204 (4%) Query: 2 NVVILDTGCANLNSVKSAIARHGYEPKVSRDPDVVLLADKLFLPGVGTAQAAMDQVRERE 61 + +I+DTGCANL+SV+ A R G + +VS D D + A ++ LPGVGTA+AAM +++++ Sbjct: 5 DTIIIDTGCANLSSVRYAFERIGADVEVSDDIDKIKAATRVVLPGVGTARAAMKALKDKK 64 Query: 62 LFDLIKACTQPVLGICLGMQLLGRRSEESNGVDL---------LGIIDEDVPKMTDFGLP 112 L D I + TQPVLG+CLGMQ+L + S+E G+ LG+ID ++ ++ GLP Sbjct: 65 LIDTICSLTQPVLGVCLGMQMLTKASQERGGLSYGNSSKDCQCLGLIDTNIEQLDAKGLP 124 Query: 113 LPHMGWNRVYPQAGNRLFQGIEDGAYFYFVHSYAMPVNPWTIAQCNYGEPFTAAVQKDNF 172 LPHMGWN++ P + LF G+ +G+Y YFVHSY P+ +TIA+C YGE F+AA+ KDNF Sbjct: 125 LPHMGWNQISPSE-HPLFAGVAEGSYVYFVHSYRAPLGDFTIAKCEYGEGFSAAIAKDNF 183 Query: 173 YGVQFHPERSGAAGAKLLKNFLEM 196 GVQFHPE+S A GA +L+NF++M Sbjct: 184 MGVQFHPEKSAAVGATILRNFMKM 207 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: 141 Number of extensions: 5 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: 224 Length adjustment: 21 Effective length of query: 175 Effective length of database: 203 Effective search space: 35525 Effective search space used: 35525 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 5209748 Shew_2201 (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.19660.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-68 214.5 0.0 1e-67 213.9 0.0 1.3 1 lcl|FitnessBrowser__PV4:5209748 Shew_2201 imidazole glycerol pho Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5209748 Shew_2201 imidazole glycerol phosphate synthase subunit HisH (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 213.9 0.0 1e-67 1e-67 2 198 .] 7 207 .. 6 207 .. 0.92 Alignments for each domain: == domain 1 score: 213.9 bits; conditional E-value: 1e-67 TIGR01855 2 vvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkpvlgiCl 79 ++id+g++Nl+sv+ a+er+ga +ev++d ++++ a+++vlPGVG++++amk l++++ l+ +++ + ++pvlg+Cl lcl|FitnessBrowser__PV4:5209748 7 IIIDTGCANLSSVRYAFERIGADVEVSDDIDKIKAATRVVLPGVGTARAAMKALKDKK--LI-DTICSLTQPVLGVCL 81 69******************************************************88..44.889************ PP TIGR01855 80 GmQllfekseE.g........kevkglglikgkvkkleaek.kvPhiGWnevevvkesellkgleeearvYfvHsYav 147 GmQ+l + s+E g k++++lgli+ ++++l+a+ ++Ph+GWn++++ +e++l++g+ e+++vYfvHsY++ lcl|FitnessBrowser__PV4:5209748 82 GMQMLTKASQErGglsygnssKDCQCLGLIDTNIEQLDAKGlPLPHMGWNQISP-SEHPLFAGVAEGSYVYFVHSYRA 158 **********953333333334689*************9999********9876.6789******************* PP TIGR01855 148 eleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknflel 198 +l + ++ak++yge f aa++kdn++gvQFHPEkS+++G+++l+nf+++ lcl|FitnessBrowser__PV4:5209748 159 PLGD--FTIAKCEYGEGFSAAIAKDNFMGVQFHPEKSAAVGATILRNFMKM 207 **97..9*****************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (224 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: 00:00:00.01 # Mc/sec: 2.56 // [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