Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_046008020.1 OLEAN_RS03120 type II 3-dehydroquinate dehydratase
Query= BRENDA::Q0VMZ2 (160 letters) >NCBI__GCF_000967895.1:WP_046008020.1 Length = 148 Score = 212 bits (539), Expect = 2e-60 Identities = 106/144 (73%), Positives = 120/144 (83%) Query: 15 LASILVLHGPNLNLLGTREPDKYGHTTLADINQQLQEQASKAGHHLQHLQSNAEYELVEC 74 + SILVL+GPNLNLLGTREP YGHTTLADI Q L +QAS AG L QSNAE+EL+E Sbjct: 1 MPSILVLNGPNLNLLGTREPGVYGHTTLADIEQSLAQQASSAGAELTSFQSNAEFELIER 60 Query: 75 IHDAHTEGVDFIIINPAAFTHTSVALRDALLAVNIPFIEVHLSNVHARETFRHHSFFSDI 134 IH A ++G+DFIIINPAAFTHTSVA+RDA+L VNIPFIEVH+SNVHARE FR HS+FSD Sbjct: 61 IHKAGSDGIDFIIINPAAFTHTSVAIRDAILGVNIPFIEVHISNVHAREDFRAHSYFSDK 120 Query: 135 AKGVICGLGAIGYALALTAALEQL 158 A GVICGLG GY AL++ALEQL Sbjct: 121 AVGVICGLGPKGYEFALSSALEQL 144 Lambda K H 0.321 0.136 0.398 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: 123 Number of extensions: 1 Number of successful extensions: 1 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: 160 Length of database: 148 Length adjustment: 17 Effective length of query: 143 Effective length of database: 131 Effective search space: 18733 Effective search space used: 18733 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 (21.9 bits) S2: 43 (21.2 bits)
Align candidate WP_046008020.1 OLEAN_RS03120 (type II 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.28741.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.7e-65 202.6 0.0 1.1e-64 202.5 0.0 1.0 1 lcl|NCBI__GCF_000967895.1:WP_046008020.1 OLEAN_RS03120 type II 3-dehydroq Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000967895.1:WP_046008020.1 OLEAN_RS03120 type II 3-dehydroquinate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 202.5 0.0 1.1e-64 1.1e-64 2 140 .. 4 143 .. 3 144 .. 0.97 Alignments for each domain: == domain 1 score: 202.5 bits; conditional E-value: 1.1e-64 TIGR01088 2 ilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeq.vdgi 69 ilvlnGPnlnlLG+rep+vyG++tl +ie+ l ++a++++ e++ fqsn e eli++ih+a + +d+i lcl|NCBI__GCF_000967895.1:WP_046008020.1 4 ILVLNGPNLNLLGTREPGVYGHTTLADIEQSLAQQASSAGAELTSFQSNAEFELIERIHKAGSDgIDFI 72 89**********************************************************98777**** PP TIGR01088 70 vinpaalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalealv 138 +inpaa+thtsva+rDa++ v++P++evh+snvhare+fr +s++++ a Gvi+GlG+kgy++al+ ++ lcl|NCBI__GCF_000967895.1:WP_046008020.1 73 IINPAAFTHTSVAIRDAILGVNIPFIEVHISNVHAREDFRAHSYFSDKAVGVICGLGPKGYEFALSSAL 141 *****************************************************************9988 PP TIGR01088 139 ea 140 e+ lcl|NCBI__GCF_000967895.1:WP_046008020.1 142 EQ 143 76 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 6.53 // [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