Align 3-dehydroquinate dehydratase; 3-dehydroquinase; Type II DHQase; EC 4.2.1.10 (characterized)
to candidate WP_010960344.1 MCA_RS05110 3-dehydroquinate dehydratase
Query= SwissProt::P43877 (154 letters) >NCBI__GCF_000008325.1:WP_010960344.1 Length = 148 Score = 198 bits (504), Expect = 3e-56 Identities = 97/141 (68%), Positives = 114/141 (80%), Gaps = 1/141 (0%) Query: 1 MKKILLLNGPNLNMLGKREPHIYGSQTLSDIEQHLQQSAQAQGYELDYFQANGEESLINR 60 M IL+LNGPNLN+LG REP IYGS TLSDIE LQ A+ G +D+FQ+N E +LI R Sbjct: 1 MAGILVLNGPNLNLLGVREPGIYGSDTLSDIESRLQAQARVAGMPIDFFQSNAEHALIER 60 Query: 61 IHQAFQNT-DFIIINPGAFTHTSVAIRDALLAVSIPFIEVHLSNVHAREPFRHHSYLSDV 119 IHQAF++ D IIINPGA THTSVA+RDALLA ++PFIEVH+SNVHAREPFR HSYLSD+ Sbjct: 61 IHQAFRDAVDMIIINPGALTHTSVALRDALLATAVPFIEVHISNVHAREPFRRHSYLSDI 120 Query: 120 AKGVICGLGAKGYDYALDFAI 140 A+GVICGLG GY+ AL A+ Sbjct: 121 ARGVICGLGPMGYELALQAAL 141 Lambda K H 0.320 0.137 0.395 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: 118 Number of extensions: 4 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: 154 Length of database: 148 Length adjustment: 16 Effective length of query: 138 Effective length of database: 132 Effective search space: 18216 Effective search space used: 18216 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 (21.8 bits) S2: 43 (21.2 bits)
Align candidate WP_010960344.1 MCA_RS05110 (3-dehydroquinate dehydratase)
to HMM TIGR01088 (aroQ: 3-dehydroquinate dehydratase, type II (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/TIGR01088.hmm # target sequence database: /tmp/gapView.22782.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01088 [M=141] Accession: TIGR01088 Description: aroQ: 3-dehydroquinate dehydratase, type II 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-65 203.5 0.0 6e-65 203.3 0.0 1.0 1 lcl|NCBI__GCF_000008325.1:WP_010960344.1 MCA_RS05110 3-dehydroquinate deh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008325.1:WP_010960344.1 MCA_RS05110 3-dehydroquinate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 203.3 0.0 6e-65 6e-65 2 139 .. 4 142 .. 3 144 .. 0.98 Alignments for each domain: == domain 1 score: 203.3 bits; conditional E-value: 6e-65 TIGR01088 2 ilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeq.vdgi 69 ilvlnGPnlnlLG rep++yGs tl +ie+ l+++a+ +++ +++fqsn e li++ih+a+ + vd i lcl|NCBI__GCF_000008325.1:WP_010960344.1 4 ILVLNGPNLNLLGVREPGIYGSDTLSDIESRLQAQARVAGMPIDFFQSNAEHALIERIHQAFRDaVDMI 72 89***********************************************************9766**** PP TIGR01088 70 vinpaalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalealv 138 +inp+althtsvalrDal+a ++P++evh+snvhare+fr++s+l+++a+Gvi+GlG+ gy+lal+a++ lcl|NCBI__GCF_000008325.1:WP_010960344.1 73 IINPGALTHTSVALRDALLATAVPFIEVHISNVHAREPFRRHSYLSDIARGVICGLGPMGYELALQAAL 141 ******************************************************************987 PP TIGR01088 139 e 139 + lcl|NCBI__GCF_000008325.1:WP_010960344.1 142 Q 142 7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (141 nodes) Target sequences: 1 (148 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: 6.04 // [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