Align 3-dehydroquinate dehydratase; 3-dehydroquinase; Type I DHQase; Type I dehydroquinase; DHQ1; EC 4.2.1.10 (characterized)
to candidate WP_012991584.1 THAL_RS02710 type I 3-dehydroquinate dehydratase
Query= SwissProt::O66440 (219 letters) >NCBI__GCF_000025605.1:WP_012991584.1 Length = 219 Score = 251 bits (640), Expect = 1e-71 Identities = 136/218 (62%), Positives = 159/218 (72%), Gaps = 4/218 (1%) Query: 1 MLIAVPLDDTNFSENLKKAKEKGADIVELRVDQFSDTSLNYVKEKLEEVHSQGLKTILTI 60 MLIAVP+ E LK+ KEKGAD++ELRVD +++ LEE H GL TILT+ Sbjct: 1 MLIAVPVTSL---EPLKECKEKGADLIELRVDLMESPTVDRALTVLEEAHRLGLGTILTV 57 Query: 61 RSPEEGGREVKNREELFEELSPLSDYTDIELSSRGLLVKLYNITKEAGKKLIISYHNFEL 120 RS EGGR++ NR ELFE+LSP SDYTDIEL+S +L ++ N AGKKLIISYHNFE Sbjct: 58 RSAREGGRDLPNRLELFEKLSPFSDYTDIELTSLDILPQVRNTVLSAGKKLIISYHNFER 117 Query: 121 TPPNWIIREVLREGYRYGG-IPKIAVKANSYEDVARLLCISRQVEGEKILISMGDYGKIS 179 TP WI++E +RE R+G I KIAVKA SY DVARLLC Q EGEKILI+MG YGKIS Sbjct: 118 TPAGWILKETIREARRWGAHIVKIAVKAESYTDVARLLCAGSQEEGEKILIAMGSYGKIS 177 Query: 180 RLAGYVFGSVITYCSLEKAFAPGQIPLEEMVELRKKFY 217 RLA +VFGSVITY L KA A GQ+PLEEMV LR+ FY Sbjct: 178 RLAAFVFGSVITYAFLGKATAEGQLPLEEMVRLREIFY 215 Lambda K H 0.317 0.137 0.382 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: 192 Number of extensions: 6 Number of successful extensions: 2 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: 219 Length of database: 219 Length adjustment: 22 Effective length of query: 197 Effective length of database: 197 Effective search space: 38809 Effective search space used: 38809 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 (21.6 bits) S2: 45 (21.9 bits)
Align candidate WP_012991584.1 THAL_RS02710 (type I 3-dehydroquinate dehydratase)
to HMM TIGR01093 (aroD: 3-dehydroquinate dehydratase, type I (EC 4.2.1.10))
# 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/TIGR01093.hmm # target sequence database: /tmp/gapView.1249.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01093 [M=229] Accession: TIGR01093 Description: aroD: 3-dehydroquinate dehydratase, type I 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-51 162.2 0.0 1.3e-51 161.9 0.0 1.0 1 lcl|NCBI__GCF_000025605.1:WP_012991584.1 THAL_RS02710 type I 3-dehydroqui Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025605.1:WP_012991584.1 THAL_RS02710 type I 3-dehydroquinate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 161.9 0.0 1.3e-51 1.3e-51 15 227 .. 10 209 .. 5 211 .. 0.94 Alignments for each domain: == domain 1 score: 161.9 bits; conditional E-value: 1.3e-51 TIGR01093 15 leelekikevgaDivElRvDllkdvsseksveavaeqlsellkdlplilTiRtqkeGGkfkgdeeerle 83 le l+++ke+gaD++ElRvDl++ + ++ ++ ++e + + l +ilT+R++ eGG+ ++ e +e lcl|NCBI__GCF_000025605.1:WP_012991584.1 10 LEPLKECKEKGADLIELRVDLMESPTVDRALTVLEEAH---RLGLGTILTVRSAREGGRDLPNRLELFE 75 67799999********************9999999999...5899************************ PP TIGR01093 84 elkeaieknlvdlvDiElkleeeavkelikeakkaktkiilSnHdfektpskeelverlekaqsldaDi 152 +l ++++d++DiEl++ + + ++ ++ a++k+i+S+H+fe+tp + l+e +++a++ +a i lcl|NCBI__GCF_000025605.1:WP_012991584.1 76 KL-----SPFSDYTDIELTSLDI-LPQVRNTVLSAGKKLIISYHNFERTPAGWILKETIREARRWGAHI 138 **.....99*********98876.556888899************************************ PP TIGR01093 153 vKiavmaksieDvltLleitlkveeekdkplialsMgekGkisRvlgavlgsvltfgslgkasAPGQis 221 vKiav+a+s++Dv++Ll++ + e ++ i++ Mg++GkisR+++ v+gsv+t++ lgka A GQ+ lcl|NCBI__GCF_000025605.1:WP_012991584.1 139 VKIAVKAESYTDVARLLCAGSQEE----GEKILIAMGSYGKISRLAAFVFGSVITYAFLGKATAEGQLP 203 ********************6665....***************************************** PP TIGR01093 222 vkelre 227 ++e+ + lcl|NCBI__GCF_000025605.1:WP_012991584.1 204 LEEMVR 209 **9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (229 nodes) Target sequences: 1 (219 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: 9.65 // [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