Align Catabolic 3-dehydroquinase; cDHQase; 3-dehydroquinate dehydratase; EC 4.2.1.10 (characterized)
to candidate HSERO_RS01935 HSERO_RS01935 3-dehydroquinate dehydratase
Query= SwissProt::P05147 (153 letters) >FitnessBrowser__HerbieS:HSERO_RS01935 Length = 145 Score = 186 bits (471), Expect = 2e-52 Identities = 88/140 (62%), Positives = 109/140 (77%), Gaps = 1/140 (0%) Query: 1 MEKSILLINGPNLNLLGTREPHIYGSTTLSDVEESSKGHAASLGASLQTFQSNHEGAIVD 60 M K +LL+NGPNLNLLGTREP +YGSTTL+D+E+ ++ A + GASL FQSNHEGA++D Sbjct: 1 MAKQLLLLNGPNLNLLGTREPAVYGSTTLADIEQRAQEQARAAGASLVAFQSNHEGALID 60 Query: 61 RIHAARGN-TDAIIINPGAYTHTSVAIRDALLGVEIPFIELHVSNVHAREPFRHHSYFSD 119 RIH AR D IIINPG THTSVA+RDAL GV IPF+E+H+SN+H RE FRH SY S Sbjct: 61 RIHQARSEGVDGIIINPGGLTHTSVALRDALAGVAIPFVEVHISNIHQREEFRHFSYLSG 120 Query: 120 KASGIIVGLGVYGYKVAVEH 139 A ++ G GV GY++AV+H Sbjct: 121 IARAVLCGFGVDGYRMAVDH 140 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: 90 Number of extensions: 2 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: 145 Length adjustment: 16 Effective length of query: 137 Effective length of database: 129 Effective search space: 17673 Effective search space used: 17673 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 HSERO_RS01935 HSERO_RS01935 (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.29374.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-62 195.3 0.0 2e-62 195.1 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS01935 HSERO_RS01935 3-dehydroquinate d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS01935 HSERO_RS01935 3-dehydroquinate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 195.1 0.0 2e-62 2e-62 2 137 .. 5 141 .. 4 145 .] 0.97 Alignments for each domain: == domain 1 score: 195.1 bits; conditional E-value: 2e-62 TIGR01088 2 ilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeq.vdg 68 +l+lnGPnlnlLG+rep+vyGs+tl +ie+ +e+a++++ ++ fqsn+eg lid+ih+a + vdg lcl|FitnessBrowser__HerbieS:HSERO_RS01935 5 LLLLNGPNLNLLGTREPAVYGSTTLADIEQRAQEQARAAGASLVAFQSNHEGALIDRIHQARSEgVDG 72 799**********************************************************9888*** PP TIGR01088 69 ivinpaalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalea 136 i+inp++lthtsvalrDala v++P+vevh+sn+h+reefr+ s+l+ +a+ v++G+G+ gy++a+ lcl|FitnessBrowser__HerbieS:HSERO_RS01935 73 IIINPGGLTHTSVALRDALAGVAIPFVEVHISNIHQREEFRHFSYLSGIARAVLCGFGVDGYRMAVDH 140 *****************************************************************976 PP TIGR01088 137 l 137 lcl|FitnessBrowser__HerbieS:HSERO_RS01935 141 W 141 5 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (141 nodes) Target sequences: 1 (145 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: 4.63 // [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