Align imidazole glycerol-phosphate synthase (subunit 1/2) (EC 4.3.2.10) (characterized)
to candidate WP_013817864.1 METME_RS05895 imidazole glycerol phosphate synthase subunit HisH
Query= BRENDA::Q5NMD4 (213 letters) >NCBI__GCF_000214665.1:WP_013817864.1 Length = 211 Score = 134 bits (338), Expect = 1e-36 Identities = 84/211 (39%), Positives = 116/211 (54%), Gaps = 16/211 (7%) Query: 9 VALIDYGAGNLRSVANALLASGLARENLVVTANPDEVLQADRVVLPGVGAFASCMQALKA 68 V +IDY AGNL +V A G + + + PDE+ + +VLPGVGAF M LK Sbjct: 4 VRVIDYDAGNLFNVVRAFEHLGCT---VKIASRPDEISDGEYLVLPGVGAFGDGMANLKK 60 Query: 69 IPDMVPALEKAVLEKGRPFLGICVGMQLLADQGEEYGVHQGLGWIKGKVTPLRPNDPSCK 128 + P LE + GRPF+GIC+GMQLL EE+G ++GLG + GKV+ L +P K Sbjct: 61 RELIAPMLEW--INTGRPFMGICLGMQLLLTSSEEFGRYEGLGIVPGKVSRLL-TEPGLK 117 Query: 129 VPHMGWNQIGLTTDS---------HPLLRAGEAYFLHSYAFVPEDESTLLATTEHG-GLV 178 VP++GW+ + D + + YF+HS+A P+D + LA + G Sbjct: 118 VPNIGWHPLSPPEDDQNRWDGTVLEGVALTRDMYFVHSFAAYPDDPAHWLAQSLFGKHWF 177 Query: 179 TAAVGRDNIMGVQFHPEKSQSYGLEFLSRFL 209 +A+ +DNI G QFHPEKS GL L FL Sbjct: 178 CSALRKDNIFGCQFHPEKSGITGLAILESFL 208 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: 145 Number of extensions: 8 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_013817864.1 METME_RS05895 (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.28311.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-60 190.0 0.0 2.4e-60 189.8 0.0 1.0 1 lcl|NCBI__GCF_000214665.1:WP_013817864.1 METME_RS05895 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000214665.1:WP_013817864.1 METME_RS05895 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 189.8 0.0 2.4e-60 2.4e-60 1 197 [. 4 209 .. 4 210 .. 0.93 Alignments for each domain: == domain 1 score: 189.8 bits; conditional E-value: 2.4e-60 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvk 69 + vidy++gNl +v +a+e++g ++++++ +e+++ + lvlPGVGaf ++m++l+++el + + + + lcl|NCBI__GCF_000214665.1:WP_013817864.1 4 VRVIDYDAGNLFNVVRAFEHLGCTVKIASRPDEISDGEYLVLPGVGAFGDGMANLKKRELIAPMLEWIN 72 579********************************************************777779999* PP TIGR01855 70 kkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek..kvPhiGWnevevvkes......ell 130 +++p++giClGmQll+ +seE ++ +glg+++gkv++l +e kvP+iGW +++ +++ ++l lcl|NCBI__GCF_000214665.1:WP_013817864.1 73 TGRPFMGICLGMQLLLTSSEEFGRYEGLGIVPGKVSRLLTEPglKVPNIGWHPLSPPEDDqnrwdgTVL 141 **************************************999899**********98876533333469* PP TIGR01855 131 kgleeearvYfvHsYaveleeeeavlakadygek.fvaavekdnivgvQFHPEkSgktGlkllknfle 197 +g+ ++YfvHs+a+++ + + la++ +g++ f +a++kdni+g+QFHPEkSg tGl++l++fl+ lcl|NCBI__GCF_000214665.1:WP_013817864.1 142 EGVALTRDMYFVHSFAAYPDDPAHWLAQSLFGKHwFCSALRKDNIFGCQFHPEKSGITGLAILESFLK 209 *******************************76538899**************************985 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 5.45 // [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