Align Catabolic 3-dehydroquinase; cDHQase; 3-dehydroquinate dehydratase; EC 4.2.1.10 (characterized)
to candidate RR42_RS32450 RR42_RS32450 3-dehydroquinate dehydratase
Query= SwissProt::P05147 (153 letters) >FitnessBrowser__Cup4G11:RR42_RS32450 Length = 150 Score = 189 bits (479), Expect = 2e-53 Identities = 92/140 (65%), Positives = 109/140 (77%), Gaps = 1/140 (0%) Query: 3 KSILLINGPNLNLLGTREPHIYGSTTLSDVEESSKGHAASLGASLQTFQSNHEGAIVDRI 62 KS+L++NGPNLNLLGTREP IYGS TL+DVE S + A LG SL FQSNHEGAIVDRI Sbjct: 2 KSVLVLNGPNLNLLGTREPQIYGSATLADVEASLRQQAGHLGLSLACFQSNHEGAIVDRI 61 Query: 63 HAARGN-TDAIIINPGAYTHTSVAIRDALLGVEIPFIELHVSNVHAREPFRHHSYFSDKA 121 HAAR I+INPGA+THTSVAIRDA GV IPF+E+H+SNVH RE FRHHSY SD A Sbjct: 62 HAARTEGVSFILINPGAFTHTSVAIRDAFAGVAIPFVEVHISNVHKREAFRHHSYLSDIA 121 Query: 122 SGIIVGLGVYGYKVAVEHVA 141 ++ G G+ GY +A++ +A Sbjct: 122 EAVMAGFGIQGYGLALQFIA 141 Lambda K H 0.317 0.134 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: 101 Number of extensions: 3 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: 153 Length of database: 150 Length adjustment: 17 Effective length of query: 136 Effective length of database: 133 Effective search space: 18088 Effective search space used: 18088 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: 42 (20.8 bits)
Align candidate RR42_RS32450 RR42_RS32450 (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.11990.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-64 200.3 0.2 5.8e-64 200.1 0.2 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS32450 RR42_RS32450 3-dehydroquinate de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS32450 RR42_RS32450 3-dehydroquinate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 200.1 0.2 5.8e-64 5.8e-64 2 140 .. 4 143 .. 3 144 .. 0.98 Alignments for each domain: == domain 1 score: 200.1 bits; conditional E-value: 5.8e-64 TIGR01088 2 ilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeq.vdgi 69 +lvlnGPnlnlLG+rep++yGs tl ++e+ l+++a +l++++ +fqsn+eg ++d+ih a + v++i lcl|FitnessBrowser__Cup4G11:RR42_RS32450 4 VLVLNGPNLNLLGTREPQIYGSATLADVEASLRQQAGHLGLSLACFQSNHEGAIVDRIHAARTEgVSFI 72 89***********************************************************9888**** PP TIGR01088 70 vinpaalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalealv 138 +inp+a+thtsva+rDa a v++P+vevh+snvh+re fr++s+l+++a+ v+ G+G++gy lal++++ lcl|FitnessBrowser__Cup4G11:RR42_RS32450 73 LINPGAFTHTSVAIRDAFAGVAIPFVEVHISNVHKREAFRHHSYLSDIAEAVMAGFGIQGYGLALQFIA 141 ******************************************************************998 PP TIGR01088 139 ea 140 + lcl|FitnessBrowser__Cup4G11:RR42_RS32450 142 AK 143 65 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (141 nodes) Target sequences: 1 (150 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: 6.65 // [ok]
This GapMind analysis is from Apr 09 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