Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_012334473.1 M446_RS22855 type II 3-dehydroquinate dehydratase
Query= BRENDA::N1V364 (155 letters) >NCBI__GCF_000019365.1:WP_012334473.1 Length = 141 Score = 149 bits (377), Expect = 1e-41 Identities = 79/139 (56%), Positives = 97/139 (69%), Gaps = 3/139 (2%) Query: 14 RKLLVLNGPNLNLLGTREPQIYGSDTLEDAET-LAARAAEAHGLAVECLQSNHEGVLIDA 72 R + VLNGPNLNLLGTREP IYG+ TL D E L ARAA+ +A+ QSNHEG L+ Sbjct: 2 RSIHVLNGPNLNLLGTREPGIYGALTLADIEARLRARAADR--VALTFRQSNHEGDLVTW 59 Query: 73 IHAARGTAAGIVINPGGYTHTSVALRDALSGVDLPVVEVHISNIHRREEFRHHSYISGIA 132 + A AG+++N G YTHTSVALRDA++G V+EVH+SN+H RE FRHHSYI+ +A Sbjct: 60 VQEAGAAGAGVILNAGAYTHTSVALRDAIAGAKAQVIEVHLSNVHARESFRHHSYIAPVA 119 Query: 133 VAVIAGAGISGYKFAVDLL 151 VIAG G Y A+D L Sbjct: 120 RGVIAGFGPLSYDLALDAL 138 Lambda K H 0.317 0.133 0.375 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: 75 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: 155 Length of database: 141 Length adjustment: 16 Effective length of query: 139 Effective length of database: 125 Effective search space: 17375 Effective search space used: 17375 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 (21.6 bits) S2: 42 (20.8 bits)
Align candidate WP_012334473.1 M446_RS22855 (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.21717.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-60 189.6 0.1 1.3e-60 189.3 0.1 1.0 1 lcl|NCBI__GCF_000019365.1:WP_012334473.1 M446_RS22855 type II 3-dehydroqu Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019365.1:WP_012334473.1 M446_RS22855 type II 3-dehydroquinate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 189.3 0.1 1.3e-60 1.3e-60 2 138 .. 4 139 .. 3 140 .. 0.97 Alignments for each domain: == domain 1 score: 189.3 bits; conditional E-value: 1.3e-60 TIGR01088 2 ilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeqvdgiv 70 i vlnGPnlnlLG+rep++yG+ltl +ie+ l++ a++ v ++++qsn+eg+l+++++ea + g++ lcl|NCBI__GCF_000019365.1:WP_012334473.1 4 IHVLNGPNLNLLGTREPGIYGALTLADIEARLRARAAD-RVALTFRQSNHEGDLVTWVQEAGAAGAGVI 71 78*******************************99876.69**************************** PP TIGR01088 71 inpaalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalealv 138 +n++a+thtsvalrDa+a +++ v+evhlsnvhare+fr++s++a+va+Gvi G+G+ +y lal al+ lcl|NCBI__GCF_000019365.1:WP_012334473.1 72 LNAGAYTHTSVALRDAIAGAKAQVIEVHLSNVHARESFRHHSYIAPVARGVIAGFGPLSYDLALDALL 139 ****************************************************************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (141 nodes) Target sequences: 1 (141 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: 4.71 // [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