Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate 7023277 Shewana3_0511 3-dehydroquinate dehydratase (RefSeq)
Query= BRENDA::A0A0H3FM50 (150 letters) >FitnessBrowser__ANA3:7023277 Length = 144 Score = 191 bits (484), Expect = 5e-54 Identities = 94/141 (66%), Positives = 110/141 (78%), Gaps = 2/141 (1%) Query: 6 RILLLNGPNLNMLGSREPEKYGSLTLAEIVNRLTAEAEALNVTLDHLQSNAEFALIDRIH 65 ++LL+NGPNLN+LG REP YG TLA+IV L+ +A+A V L+H+QSNAEF LI+ IH Sbjct: 4 KVLLINGPNLNLLGRREPSVYGHQTLADIVALLSEQAQAAGVELEHIQSNAEFELINAIH 63 Query: 66 QAKDSVDYILINPAAFTHTSVAIRDALLAVSIPFIEIHLSNVHAREPFRHHSYLSDVASG 125 I+INPAAFTHTSVA+RDALL V IPF E+HLSNVHAREPFRHHSYLSD A G Sbjct: 64 AT--DAQMIIINPAAFTHTSVALRDALLGVDIPFFEVHLSNVHAREPFRHHSYLSDKAIG 121 Query: 126 VICGLGADGYSYALQTAVKRL 146 VICG GA GY +AL A+KRL Sbjct: 122 VICGFGAQGYEFALAAAIKRL 142 Lambda K H 0.320 0.134 0.379 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: 100 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: 150 Length of database: 144 Length adjustment: 16 Effective length of query: 134 Effective length of database: 128 Effective search space: 17152 Effective search space used: 17152 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: 42 (20.8 bits)
Align candidate 7023277 Shewana3_0511 (3-dehydroquinate dehydratase (RefSeq))
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.10552.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-63 198.7 0.2 1.8e-63 198.5 0.2 1.0 1 lcl|FitnessBrowser__ANA3:7023277 Shewana3_0511 3-dehydroquinate d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7023277 Shewana3_0511 3-dehydroquinate dehydratase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 198.5 0.2 1.8e-63 1.8e-63 1 140 [. 4 141 .. 4 142 .. 0.98 Alignments for each domain: == domain 1 score: 198.5 bits; conditional E-value: 1.8e-63 TIGR01088 1 kilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeqvdgivinpaalt 77 k+l++nGPnlnlLG+rep+vyG++tl +i++ll+e+a++++ve+e++qsn e eli++ih + ++ i+inpaa+t lcl|FitnessBrowser__ANA3:7023277 4 KVLLINGPNLNLLGRREPSVYGHQTLADIVALLSEQAQAAGVELEHIQSNAEFELINAIHATD--AQMIIINPAAFT 78 699*********************************************************988..789********* PP TIGR01088 78 htsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalealvea 140 htsvalrDal+ v +P+ evhlsnvhare+fr++s+l++ a Gvi+G+Ga+gy++al a+++ lcl|FitnessBrowser__ANA3:7023277 79 HTSVALRDALLGVDIPFFEVHLSNVHAREPFRHHSYLSDKAIGVICGFGAQGYEFALAAAIKR 141 *********************************************************999875 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.42 // [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