Align periplasmic dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate Pf6N2E2_5062 3-dehydroquinate dehydratase II (EC 4.2.1.10)
Query= metacyc::MONOMER-15328 (160 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5062 Length = 147 Score = 181 bits (460), Expect = 3e-51 Identities = 82/143 (57%), Positives = 108/143 (75%) Query: 15 PLITVLNGPNLNMLGLRQPGIYGHATLDDVEQVCIQAAERLDVAIDFRQTNGEGELVSWV 74 P++ VLNGPNLN+LG R+P YGH TL D+ +C +AAE +A++FRQTN EGEL+ W+ Sbjct: 3 PIVLVLNGPNLNLLGTREPATYGHETLADISALCGRAAEEFGLAVEFRQTNQEGELLDWI 62 Query: 75 QECRGRADGIVINPAAYGHTSIALLDALLAVELPVIEVHISNIHRREPFRHHTYVSQAAI 134 RGR GIVINPAA+ HTS+A+ DAL+A E+PVIEVH+SN+H RE FRHH++VS AI Sbjct: 63 HGARGRCAGIVINPAAWTHTSVAIRDALVASEVPVIEVHLSNVHARETFRHHSFVSSVAI 122 Query: 135 GVICGLGVRGYAHALQAITDMIE 157 GV+CG G GY AL+ + ++ Sbjct: 123 GVMCGFGSHGYRLALEHFSQRLK 145 Lambda K H 0.322 0.139 0.414 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: 120 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: 160 Length of database: 147 Length adjustment: 17 Effective length of query: 143 Effective length of database: 130 Effective search space: 18590 Effective search space used: 18590 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 Pf6N2E2_5062 (3-dehydroquinate dehydratase II (EC 4.2.1.10))
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.18255.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-63 197.3 0.0 4.7e-63 197.2 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5062 3-dehydroquinate dehydratase II Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5062 3-dehydroquinate dehydratase II (EC 4.2.1.10) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 197.2 0.0 4.7e-63 4.7e-63 2 139 .. 5 142 .. 4 144 .. 0.98 Alignments for each domain: == domain 1 score: 197.2 bits; conditional E-value: 4.7e-63 TIGR01088 2 ilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeq 65 +lvlnGPnlnlLG+rep+ yG+ tl +i++l+ +aa+e ++ ve++q+n+egel+d+ih a ++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5062 5 VLVLNGPNLNLLGTREPATYGHETLADISALCGRAAEEFGLAVEFRQTNQEGELLDWIHGARGR 68 89************************************************************** PP TIGR01088 66 vdgivinpaalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakg 129 givinpaa+thtsva+rDal+a ++Pv+evhlsnvhare fr++s+++ va Gv++G+G +g lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5062 69 CAGIVINPAAWTHTSVAIRDALVASEVPVIEVHLSNVHARETFRHHSFVSSVAIGVMCGFGSHG 132 **************************************************************** PP TIGR01088 130 yklalealve 139 y+lale + lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5062 133 YRLALEHFSQ 142 *****98765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (141 nodes) Target sequences: 1 (147 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: 4.91 // [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