Align Imidazole glycerol phosphate synthase subunit HisH 2; EC 4.3.2.10; IGP synthase glutaminase subunit 2; EC 3.5.1.2; IGP synthase subunit HisH 2; ImGP synthase subunit HisH 2; IGPS subunit HisH 2 (uncharacterized)
to candidate WP_011802493.1 PNAP_RS15620 imidazole glycerol phosphate synthase subunit HisH
Query= curated2:P61783 (202 letters) >NCBI__GCF_000015505.1:WP_011802493.1 Length = 202 Score = 191 bits (486), Expect = 6e-54 Identities = 98/201 (48%), Positives = 133/201 (66%), Gaps = 3/201 (1%) Query: 1 MIAIIDYGMGNVGSIKNMIAKIGFDAIITNDPELISKATKLILPGVGSFDSGMTNLKELG 60 MI I+DY GN+ S+ NMI K G DA ++ E+I +A+KLILPGVG++D GM++L Sbjct: 1 MIVIVDYECGNIASVLNMIRKAGGDATVSGSHEVIQQASKLILPGVGAYDQGMSHLHAKQ 60 Query: 61 LIDILNKKVVQEKTPLLGICLGMHLLTNSSEEGRLKGLGFINA--KTVKFKLSNKFKIPH 118 L IL + PLLGICLGM LL SEEG++ GLG I A K F + +IPH Sbjct: 61 LPAILQARAAAG-VPLLGICLGMQLLGLGSEEGKIPGLGLIAARFKRFVFNADSAMRIPH 119 Query: 119 MGWNYVKFSIKNKLSDNLIENSRFYFVHSYYVICEDKKNILMTTEYENEFTSAVSKDNIY 178 +GWN V N+L + E R+YF HSYY +C +++IL TTEY + F SA S++++Y Sbjct: 120 VGWNTVYAKKINRLISDDQEEKRYYFDHSYYAVCAHEEDILATTEYGHGFPSAYSRESVY 179 Query: 179 GVQFHPEKSHKFGMKLMENFI 199 GVQFHPEKSH+FG+ L++ F+ Sbjct: 180 GVQFHPEKSHRFGLSLIKQFL 200 Lambda K H 0.320 0.138 0.396 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: 143 Number of extensions: 6 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: 202 Length of database: 202 Length adjustment: 21 Effective length of query: 181 Effective length of database: 181 Effective search space: 32761 Effective search space used: 32761 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 (21.8 bits) S2: 45 (21.9 bits)
Align candidate WP_011802493.1 PNAP_RS15620 (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.24555.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-65 206.3 0.0 2.3e-65 206.2 0.0 1.0 1 lcl|NCBI__GCF_000015505.1:WP_011802493.1 PNAP_RS15620 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015505.1:WP_011802493.1 PNAP_RS15620 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 206.2 0.0 2.3e-65 2.3e-65 1 197 [. 2 201 .. 2 202 .] 0.97 Alignments for each domain: == domain 1 score: 206.2 bits; conditional E-value: 2.3e-65 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvk 69 iv++dy++gN++sv ++++++g ++v+ +++ +++a kl+lPGVGa++++m++l+ ++l ++ + +++ lcl|NCBI__GCF_000015505.1:WP_011802493.1 2 IVIVDYECGNIASVLNMIRKAGGDATVSGSHEVIQQASKLILPGVGAYDQGMSHLHAKQLPAILQARAA 70 89*********************************************************99999***** PP TIGR01855 70 kkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek....kvPhiGWnevevvkesellkgle 134 ++ p+lgiClGmQll seEg + +glgli + k++ + ++Ph+GWn+v +k ++l+++ + lcl|NCBI__GCF_000015505.1:WP_011802493.1 71 AGVPLLGICLGMQLLGLGSEEG-KIPGLGLIAARFKRFVFNAdsamRIPHVGWNTVYAKKINRLISDDQ 138 *********************6.69************987766789*********************** PP TIGR01855 135 eearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 ee+r+Yf HsY++++++ee++la+++yg+ f++a +++ ++gvQFHPEkS+++Gl+l+k+fl+ lcl|NCBI__GCF_000015505.1:WP_011802493.1 139 EEKRYYFDHSYYAVCAHEEDILATTEYGHGFPSAYSRESVYGVQFHPEKSHRFGLSLIKQFLD 201 ************************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (202 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 5.58 // [ok]
This GapMind analysis is from Apr 10 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