Align imidazole glycerol-phosphate synthase (subunit 1/2) (EC 4.3.2.10) (characterized)
to candidate WP_085217753.1 B9N75_RS04735 imidazole glycerol phosphate synthase subunit HisH
Query= BRENDA::Q5NMD4 (213 letters) >NCBI__GCF_900177405.1:WP_085217753.1 Length = 205 Score = 137 bits (345), Expect = 1e-37 Identities = 86/206 (41%), Positives = 118/206 (57%), Gaps = 12/206 (5%) Query: 9 VALIDYGAGNLRSVANALLASGLARENLVVTANPDEVLQADRVVLPGVGAFASCMQALKA 68 V ++D G GN++SV A+ E + ++P + R+ LPGVGAF + M AL Sbjct: 3 VTIVDCGIGNIKSVERMFQAADATAE---IVSDPASLKDCRRLALPGVGAFDAGMAALN- 58 Query: 69 IPDMVPALEKAVLEKGRPFLGICVGMQLLADQGEEYGVHQGLGWIKGKVTPLR-PNDPSC 127 AL++ LE+ P LGIC+GMQLL +G E G GLGWI G V L + + Sbjct: 59 -DGWRAALDQVALERRIPVLGICLGMQLLC-RGSEEGEAAGLGWIAGDVVTLDLGGNAAL 116 Query: 128 KVPHMGWNQIGLTTDSHPLLR--AGEA--YFLHSYAFVPEDESTLLATTEHGGLVTAAVG 183 ++PHMGW+ + ++PL+ AGE Y +H Y V + E +LATTE+G AV Sbjct: 117 RLPHMGWSVV-TPARNNPLIPSDAGEQRFYHVHKYRAVCDREEDVLATTEYGTRFVTAVQ 175 Query: 184 RDNIMGVQFHPEKSQSYGLEFLSRFL 209 RDNI GVQFHPEKS +GL+ + FL Sbjct: 176 RDNIFGVQFHPEKSHRFGLQLMRNFL 201 Lambda K H 0.318 0.136 0.409 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: 154 Number of extensions: 14 Number of successful extensions: 6 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: 213 Length of database: 205 Length adjustment: 21 Effective length of query: 192 Effective length of database: 184 Effective search space: 35328 Effective search space used: 35328 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 45 (21.9 bits)
Align candidate WP_085217753.1 B9N75_RS04735 (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.1985910.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-67 212.7 0.0 2.6e-67 212.5 0.0 1.0 1 NCBI__GCF_900177405.1:WP_085217753.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900177405.1:WP_085217753.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 212.5 0.0 2.6e-67 2.6e-67 1 197 [. 3 202 .. 3 203 .. 0.95 Alignments for each domain: == domain 1 score: 212.5 bits; conditional E-value: 2.6e-67 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkp 73 ++++d g+gN+ksv++++++++a++e+v+d +l+++ +l lPGVGaf+++m+ l++ + +l + + +++ p NCBI__GCF_900177405.1:WP_085217753.1 3 VTIVDCGIGNIKSVERMFQAADATAEIVSDPASLKDCRRLALPGVGAFDAGMAALNDGWRAALDQVALERRIP 75 689*****************************************************988899988999999** PP TIGR01855 74 vlgiClGmQllfekseEgkevkglglikgkvkkleaek....kvPhiGWnevevvkesellkgleeearvYfv 142 vlgiClGmQll + seEg e+ glg+i g+v+ l+ ++Ph+GW v+++++++l+ e+r+Y+v NCBI__GCF_900177405.1:WP_085217753.1 76 VLGICLGMQLLCRGSEEG-EAAGLGWIAGDVVTLDLGGnaalRLPHMGWSVVTPARNNPLIPSDAGEQRFYHV 147 *****************6.68************975544567********************99999****** PP TIGR01855 143 HsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 H Y++++ ee+vla+++yg++fv+av++dni+gvQFHPEkS+++Gl+l++nfl+ NCBI__GCF_900177405.1:WP_085217753.1 148 HKYRAVCDREEDVLATTEYGTRFVTAVQRDNIFGVQFHPEKSHRFGLQLMRNFLA 202 *****************************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (205 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: 13.61 // [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