Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_013683138.1 ARCVE_RS02145 type I 3-dehydroquinate dehydratase
Query= BRENDA::O30011 (196 letters) >NCBI__GCF_000194625.1:WP_013683138.1 Length = 197 Score = 202 bits (513), Expect = 4e-57 Identities = 107/200 (53%), Positives = 137/200 (68%), Gaps = 9/200 (4%) Query: 1 MKLVATLSSPEELELAEKADVVELRIDLFDFSGA-----RVDKEKILTCRRVSDGGKFEG 55 MK+V + S +E + DVVELR+DLFD A + KEKI+T RR +GG FEG Sbjct: 1 MKIVVSARSLQEAKA--DCDVVELRLDLFDRLPAISEVEAISKEKIVTVRRKDEGGLFEG 58 Query: 56 DERERIEKMKRAFDSLNPDYVDLESDLPDSAFDFNCRIIESYHNFIRTPDYSELKGIVEG 115 E ER+E M++ N YVD+E D D FD C+IIESYHNF TP + L+ ++EG Sbjct: 59 SEEERLELMRKYATVAN--YVDVECDAHDDFFDMPCKIIESYHNFSETPPFETLRDMIEG 116 Query: 116 RRGDLVKIATMGKSKRDVETIVRILTNYDDVVAFLMGERFSFTRVLAAYLGSPFIYCYVG 175 RRGD+ KIAT+G+ KRDV TIVRIL YD+VVAFLMGE+F++TR+LA LGSPFIYC+ G Sbjct: 117 RRGDIFKIATLGRDKRDVLTIVRILCEYDNVVAFLMGEKFAYTRILAVMLGSPFIYCHAG 176 Query: 176 SPKAPGQISLDDAREIISRL 195 + APGQ+ AR+I+ L Sbjct: 177 NAVAPGQLEAGKARKILEML 196 Lambda K H 0.321 0.140 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: 146 Number of extensions: 7 Number of successful extensions: 3 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: 196 Length of database: 197 Length adjustment: 20 Effective length of query: 176 Effective length of database: 177 Effective search space: 31152 Effective search space used: 31152 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 (21.8 bits) S2: 45 (21.9 bits)
Align candidate WP_013683138.1 ARCVE_RS02145 (type I 3-dehydroquinate dehydratase)
to HMM TIGR01093 (aroD: 3-dehydroquinate dehydratase, type I (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/TIGR01093.hmm # target sequence database: /tmp/gapView.26313.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01093 [M=229] Accession: TIGR01093 Description: aroD: 3-dehydroquinate dehydratase, type I 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-49 155.1 0.0 2e-49 154.8 0.0 1.1 1 lcl|NCBI__GCF_000194625.1:WP_013683138.1 ARCVE_RS02145 type I 3-dehydroqu Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000194625.1:WP_013683138.1 ARCVE_RS02145 type I 3-dehydroquinate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 154.8 0.0 2e-49 2e-49 17 228 .. 9 192 .. 2 193 .. 0.93 Alignments for each domain: == domain 1 score: 154.8 bits; conditional E-value: 2e-49 TIGR01093 17 elekikevgaDivElRvDllkdvsseksveavaeqlsellkdlplilTiRtqkeGGkfkgdeeerleel 85 l+++k ++D+vElR+Dl++ + + ++vea+ +++ i+T+R++ eGG f+g+eeerle++ lcl|NCBI__GCF_000194625.1:WP_013683138.1 9 SLQEAK-ADCDVVELRLDLFDRLPAISEVEAI---------SKEKIVTVRRKDEGGLFEGSEEERLELM 67 566756.8*****************9866554.........4677************************ PP TIGR01093 86 keaieknlvdlvDiElkleeeavkelikeakkaktkiilSnHdfektpskeelverlekaqsldaDivK 154 ++++ ++vD+E ++++++ + +kii S+H+f++tp+ e l++++e ++ +Di K lcl|NCBI__GCF_000194625.1:WP_013683138.1 68 RKYATVA--NYVDVECDAHDDFF--------DMPCKIIESYHNFSETPPFETLRDMIEGRR---GDIFK 123 ***9876..9***********77........4789************************99...***** PP TIGR01093 155 iavmaksieDvltLleitlkveeekdkplialsMgekGkisRvlgavlgsvltfgslgkasAPGQisvk 223 ia+ +++++Dvlt+++i+ +++ +++a+ Mgek++ +R+l+ +lgs ++++++g+a APGQ++ lcl|NCBI__GCF_000194625.1:WP_013683138.1 124 IATLGRDKRDVLTIVRILCEYD-----NVVAFLMGEKFAYTRILAVMLGSPFIYCHAGNAVAPGQLEAG 187 *********************8.....9***************************************99 PP TIGR01093 224 elrel 228 + r++ lcl|NCBI__GCF_000194625.1:WP_013683138.1 188 KARKI 192 99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (229 nodes) Target sequences: 1 (197 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: 7.97 // [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