Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate YP_004142729.1 Mesci_3559 3-dehydroquinate dehydratase
Query= BRENDA::W6JLW3 (160 letters) >NCBI__GCF_000185905.1:YP_004142729.1 Length = 144 Score = 160 bits (406), Expect = 6e-45 Identities = 82/137 (59%), Positives = 97/137 (70%), Gaps = 1/137 (0%) Query: 17 ITVLNGPNLNMLGLRQPGIYGHATLDDVEQVCIQAAERLDVAIDFRQTNGEGELVSWVQE 76 + VLNGPNLN LG R+PGIYG TL + C QA L IDFRQ+N EG+LV W+QE Sbjct: 4 VFVLNGPNLNALGKREPGIYGGKTLAAIADDCKQAGTALGFEIDFRQSNHEGDLVDWIQE 63 Query: 77 CRGRADGIVINPAAYGHTSIALLDALLAV-ELPVVEVHISNIHRREPFRHHTYVSQAAIG 135 +A GIVINP AY HTSIA+ DA+ AV LPV EVH+SNIH REPFRH + V+ A+G Sbjct: 64 AGDKAVGIVINPGAYSHTSIAIHDAIRAVAPLPVAEVHLSNIHAREPFRHVSMVAPVAVG 123 Query: 136 VICGLGVRGYAHALQAI 152 +ICG G GY ALQA+ Sbjct: 124 MICGFGPLGYTLALQAL 140 Lambda K H 0.322 0.139 0.413 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: 102 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: 160 Length of database: 144 Length adjustment: 17 Effective length of query: 143 Effective length of database: 127 Effective search space: 18161 Effective search space used: 18161 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 YP_004142729.1 Mesci_3559 (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.22124.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-61 190.4 0.0 6.4e-61 190.2 0.0 1.0 1 lcl|NCBI__GCF_000185905.1:YP_004142729.1 Mesci_3559 3-dehydroquinate dehy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000185905.1:YP_004142729.1 Mesci_3559 3-dehydroquinate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 190.2 0.0 6.4e-61 6.4e-61 2 139 .. 4 142 .. 3 144 .] 0.97 Alignments for each domain: == domain 1 score: 190.2 bits; conditional E-value: 6.4e-61 TIGR01088 2 ilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeqvdgiv 70 + vlnGPnln LGkrep++yG tl i + +++a+++l+ e++++qsn+eg+l+d+i+ea +++ giv lcl|NCBI__GCF_000185905.1:YP_004142729.1 4 VFVLNGPNLNALGKREPGIYGGKTLAAIADDCKQAGTALGFEIDFRQSNHEGDLVDWIQEAGDKAVGIV 72 78******************************************************************* PP TIGR01088 71 inpaalthtsvalrDalaavs.lPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalealv 138 inp+a++hts+a+ Da+ av+ lPv evhlsn+hare+fr+ s++a+va G+i+G+G+ gy+lal+al+ lcl|NCBI__GCF_000185905.1:YP_004142729.1 73 INPGAYSHTSIAIHDAIRAVApLPVAEVHLSNIHAREPFRHVSMVAPVAVGMICGFGPLGYTLALQALA 141 *****************998659*******************************************997 PP TIGR01088 139 e 139 lcl|NCBI__GCF_000185905.1:YP_004142729.1 142 A 142 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (141 nodes) Target sequences: 1 (144 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: 5.38 // [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