Align imidazole glycerol-phosphate synthase (subunit 1/2) (EC 4.3.2.10) (characterized)
to candidate WP_051622994.1 P166_RS0105455 imidazole glycerol phosphate synthase subunit HisH
Query= BRENDA::Q5NMD4 (213 letters) >NCBI__GCF_000711315.1:WP_051622994.1 Length = 211 Score = 145 bits (367), Expect = 4e-40 Identities = 93/214 (43%), Positives = 122/214 (57%), Gaps = 16/214 (7%) Query: 6 SSTVALIDYGAGNLRSVANALLASGLARENLVVTANPDEVLQADRVVLPGVGAFASCMQA 65 S+ V +IDYGAGNL +V A G E + P++V QADR+V PGVGAF MQ Sbjct: 2 SAKVTIIDYGAGNLLNVQRAFEHQGAQTE---IATTPEQVEQADRLVFPGVGAFPEAMQQ 58 Query: 66 LKAIPDMVPALEKAVLEKGRPFLGICVGMQLLADQGEEYGVHQGLGWIKGKVTPLRPNDP 125 LK ++V A++ A +K PFLGIC+GMQ++ ++ EE+G +GL + GKV L Sbjct: 59 LKT-QNLVEAIQIAAEQK--PFLGICLGMQMMLEESEEFGTTEGLKLLPGKVRKLPETSI 115 Query: 126 S---CKVPHMGWNQI--GLTTDSHPLL----RAGEAYFLHSYAFVPEDESTLLATTEHGG 176 S +PHMGW QI T + LL YF+HSY +E+ LA + GG Sbjct: 116 SGEIMTIPHMGWAQIRPNKTPWQNSLLTSVPETNAFYFVHSYFADVANETDQLAVFDFGG 175 Query: 177 -LVTAAVGRDNIMGVQFHPEKSQSYGLEFLSRFL 209 +TAAV +DN MG QFHPEKS GL + FL Sbjct: 176 HAITAAVQQDNRMGCQFHPEKSGEMGLRLIEAFL 209 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: 151 Number of extensions: 10 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: 211 Length adjustment: 21 Effective length of query: 192 Effective length of database: 190 Effective search space: 36480 Effective search space used: 36480 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_051622994.1 P166_RS0105455 (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.11075.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-69 218.1 0.0 5.8e-69 217.9 0.0 1.0 1 lcl|NCBI__GCF_000711315.1:WP_051622994.1 P166_RS0105455 imidazole glycero Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000711315.1:WP_051622994.1 P166_RS0105455 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 217.9 0.0 5.8e-69 5.8e-69 1 197 [. 5 210 .. 5 211 .] 0.95 Alignments for each domain: == domain 1 score: 217.9 bits; conditional E-value: 5.8e-69 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrele.lellaekvv 68 +++idyg+gNl +v++a+e+ ga++e++++ +++e+ad+lv+PGVGaf eam++l+ ++ +e++ +++ lcl|NCBI__GCF_000711315.1:WP_051622994.1 5 VTIIDYGAGNLLNVQRAFEHQGAQTEIATTPEQVEQADRLVFPGVGAFPEAMQQLKTQNlVEAI--QIA 71 68*********************************************************56666..999 PP TIGR01855 69 kkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek......kvPhiGWnevevvk...ese 128 +++kp+lgiClGmQ+++e+seE ++++gl l++gkv+kl ++ ++Ph+GW ++ + k +++ lcl|NCBI__GCF_000711315.1:WP_051622994.1 72 AEQKPFLGICLGMQMMLEESEEFGTTEGLKLLPGKVRKLPETSisgeimTIPHMGWAQIRPNKtpwQNS 140 9**************************************9998899999**********9887333679 PP TIGR01855 129 llkgleeearvYfvHsYaveleeeeavlakady.gekfvaavekdnivgvQFHPEkSgktGlkllknfl 196 ll+ + e + +YfvHsY + +++e + la d+ g+ ++aav++dn +g+QFHPEkSg++Gl+l++ fl lcl|NCBI__GCF_000711315.1:WP_051622994.1 141 LLTSVPETNAFYFVHSYFADVANETDQLAVFDFgGHAITAAVQQDNRMGCQFHPEKSGEMGLRLIEAFL 209 *********************************7789*****************************998 PP TIGR01855 197 e 197 + lcl|NCBI__GCF_000711315.1:WP_051622994.1 210 K 210 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (211 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: 5.74 // [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