Align IGP synthase glutamine amidotransferase subunit; EC 2.4.2.- (characterized)
to candidate WP_010527315.1 GQW_RS0107145 imidazole glycerol phosphate synthase subunit HisH
Query= CharProtDB::CH_024511 (196 letters) >NCBI__GCF_000220155.1:WP_010527315.1 Length = 200 Score = 169 bits (429), Expect = 2e-47 Identities = 89/201 (44%), Positives = 123/201 (61%), Gaps = 7/201 (3%) Query: 1 MNVVILDTGCANLNSVKSAIARHGYEPKVSRDPDVVLLADKLFLPGVGTAQAAMDQVRER 60 MN+ I+ N+ SV A+ R GY+P ++ D D + ADK+ PGVG A M +++ Sbjct: 1 MNIAIIKYNAGNIRSVSFALERLGYKPIITGDHDTIRKADKVIFPGVGEASTTMAFLKQN 60 Query: 61 ELFDLIKACTQPVLGICLGMQLLGRRSEESNGVDLLGIIDEDVPKMTDFG-----LPLPH 115 L +LI + TQPVLGICLG+QL+ + SEE + + LGI + V K +PH Sbjct: 61 GLHELIPSLTQPVLGICLGLQLMCKYSEEGD-TECLGIFNAPVKKFIPLKDVSPKQKIPH 119 Query: 116 MGWNRVYPQAGNRLFQGIEDGAYFYFVHSYAMPVNPWTIAQCNYGEPFTAAVQKDNFYGV 175 MGWN + + LF +G + YFVHSY +P TIAQ NY PF+AA+QKDNF+ Sbjct: 120 MGWNNL-THVKSPLFNPELEGEFVYFVHSYYVPTGAETIAQANYIHPFSAALQKDNFFAT 178 Query: 176 QFHPERSGAAGAKLLKNFLEM 196 QFHPE+SG+ G ++LKNFL + Sbjct: 179 QFHPEKSGSVGEQILKNFLSL 199 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: 127 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: 200 Length adjustment: 20 Effective length of query: 176 Effective length of database: 180 Effective search space: 31680 Effective search space used: 31680 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 WP_010527315.1 GQW_RS0107145 (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.2884145.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-64 202.5 0.0 3.3e-64 202.4 0.0 1.0 1 NCBI__GCF_000220155.1:WP_010527315.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000220155.1:WP_010527315.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 202.4 0.0 3.3e-64 3.3e-64 1 197 [. 3 198 .. 3 199 .. 0.92 Alignments for each domain: == domain 1 score: 202.4 bits; conditional E-value: 3.3e-64 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkp 73 i++i y++gN++sv+ aler+g+++ ++ d+++++kadk+++PGVG+++ +m+ l++++ l+e + + ++p NCBI__GCF_000220155.1:WP_010527315.1 3 IAIIKYNAGNIRSVSFALERLGYKPIITGDHDTIRKADKVIFPGVGEASTTMAFLKQNG---LHELIPSLTQP 72 79*******************************************************99...45668999*** PP TIGR01855 74 vlgiClGmQllfekseEgkevkglglikgkvkkleaek......kvPhiGWnevevvkesellkgleeearvY 140 vlgiClG+Ql+ + seEg ++++lg+++ vkk+ k k+Ph+GWn+++ vk+ +l++ e++ vY NCBI__GCF_000220155.1:WP_010527315.1 73 VLGICLGLQLMCKYSEEG-DTECLGIFNAPVKKFIPLKdvspkqKIPHMGWNNLTHVKS-PLFNPELEGEFVY 143 *****************7.68************86544456777********9998875.57776667889** PP TIGR01855 141 fvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 fvHsY+v++ +++a+a+y + f aa++kdn++++QFHPEkSg++G ++lknfl+ NCBI__GCF_000220155.1:WP_010527315.1 144 FVHSYYVPTGA--ETIAQANYIHPFSAALQKDNFFATQFHPEKSGSVGEQILKNFLS 198 ********997..79****************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (200 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: 14.85 // [ok]
This GapMind analysis is from Jul 26 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