Align IGP synthase glutamine amidotransferase subunit; EC 2.4.2.- (characterized)
to candidate WP_066326536.1 BLR17_RS14000 imidazole glycerol phosphate synthase subunit HisH
Query= CharProtDB::CH_024511 (196 letters) >NCBI__GCF_900100165.1:WP_066326536.1 Length = 193 Score = 158 bits (399), Expect = 7e-44 Identities = 84/196 (42%), Positives = 120/196 (61%), Gaps = 3/196 (1%) Query: 1 MNVVILDTGCANLNSVKSAIARHGYEPKVSRDPDVVLLADKLFLPGVGTAQAAMDQVRER 60 M +VI++ G N+ S+ AI R G+ ++ +PD + ADK+ PGVG A AM ++E Sbjct: 1 MKIVIINYGAGNIQSILFAIERLGFTAVLTNNPDEIKAADKVIFPGVGEASYAMKMLKES 60 Query: 61 ELFDLIKACTQPVLGICLGMQLLGRRSEESNGVDLLGIIDEDVPKMTDFGLPLPHMGWNR 120 L LI QPVLGICLGMQL+ +EE + LGI D DV K T + +P MGWN Sbjct: 61 GLDTLIPTLKQPVLGICLGMQLMCNHTEEGDTTG-LGIFDVDVTKFTP-KVKVPQMGWNT 118 Query: 121 VYPQAGNRLFQGIEDGAYFYFVHSYAMPVNPWTIAQCNYGEPFTAAVQKDNFYGVQFHPE 180 +Y + LF+ + + Y Y VHS+ P+ TIA +Y P+++A++ NFYG QFHPE Sbjct: 119 IYDLKSD-LFKDVAEKEYMYLVHSFYAPLCEETIATTDYELPYSSALENGNFYGTQFHPE 177 Query: 181 RSGAAGAKLLKNFLEM 196 +SG G ++L NFL++ Sbjct: 178 KSGDMGEQILGNFLKL 193 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: 132 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: 193 Length adjustment: 20 Effective length of query: 176 Effective length of database: 173 Effective search space: 30448 Effective search space used: 30448 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: 44 (21.6 bits)
Align candidate WP_066326536.1 BLR17_RS14000 (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.1188119.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-67 210.9 0.0 8.8e-67 210.8 0.0 1.0 1 NCBI__GCF_900100165.1:WP_066326536.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900100165.1:WP_066326536.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 210.8 0.0 8.8e-67 8.8e-67 1 197 [. 3 192 .. 3 193 .] 0.96 Alignments for each domain: == domain 1 score: 210.8 bits; conditional E-value: 8.8e-67 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkp 73 iv+i+yg+gN++s+ a+er+g++++++++ +e++ adk+++PGVG+++ amk l+e++l++l + + k+p NCBI__GCF_900100165.1:WP_066326536.1 3 IVIINYGAGNIQSILFAIERLGFTAVLTNNPDEIKAADKVIFPGVGEASYAMKMLKESGLDTL---IPTLKQP 72 89*********************************************************7777...889999* PP TIGR01855 74 vlgiClGmQllfekseEgkevkglglikgkvkkleaekkvPhiGWnevevvkesellkgleeearvYfvHsYa 146 vlgiClGmQl+ +++eEg +++glg+++ +v+k++ ++kvP++GWn++ +k+ +l+k++ e++++Y vHs++ NCBI__GCF_900100165.1:WP_066326536.1 73 VLGICLGMQLMCNHTEEG-DTTGLGIFDVDVTKFTPKVKVPQMGWNTIYDLKS-DLFKDVAEKEYMYLVHSFY 143 *****************7.68*************************8887765.5****************** PP TIGR01855 147 veleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 ++l e +++a++dy+ + +a+e++n++g+QFHPEkSg++G ++l nfl+ NCBI__GCF_900100165.1:WP_066326536.1 144 APLCE--ETIATTDYELPYSSALENGNFYGTQFHPEKSGDMGEQILGNFLK 192 ***98..799***************************************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (193 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.55 // [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