Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_012968942.1 KVAR_RS21480 3-dehydroquinase
Query= BRENDA::P24670 (252 letters) >NCBI__GCF_000025465.1:WP_012968942.1 Length = 251 Score = 269 bits (688), Expect = 4e-77 Identities = 139/246 (56%), Positives = 174/246 (70%) Query: 4 VTVKNLIIGEGMPKIIVSLMGRDINSVKAEALAYREATFDILEWRVDHFMDIASTQSVLT 63 VTVKN+ EG I V L+G+ ++ + A +A DI+EWRVDHF + V+ Sbjct: 5 VTVKNITFQEGETLICVPLIGKTLDEILGNAHGLVDAGADIIEWRVDHFTQVRDMTQVMA 64 Query: 64 AARVIRDAMPDIPLLFTFRSAKEGGEQTITTQHYLTLNRAAIDSGLVDMIDLELFTGDAD 123 A IR A+ +PLLFTFRS KEGGE I+ + Y LNR A SGLVD+ID+ELF +A Sbjct: 65 ALAEIRGALKALPLLFTFRSKKEGGETEISDEAYFALNREAARSGLVDVIDIELFNDEAQ 124 Query: 124 VKATVDYAHAHNVYVVMSNHDFHQTPSAEEMVLRLRKMQALGADIPKIAVMPQSKHDVLT 183 ++A VD AHA V V+MSNHDFH+TP+ E+++ RLR+MQ LGAD+PKIAVMPQS DVLT Sbjct: 125 IRALVDDAHAAGVKVIMSNHDFHKTPAQEDIIYRLRRMQDLGADLPKIAVMPQSPQDVLT 184 Query: 184 LLTATLEMQQHYADRPVITMSMAKEGVISRLAGEVFGSAATFGAVKQASAPGQIAVNDLR 243 LL ATL M++ YA RP+ITMSM K G +SR+ G +FGSA TFG V QASAPGQIA+ LR Sbjct: 185 LLAATLTMKEKYATRPLITMSMGKSGGVSRVTGRLFGSAMTFGTVGQASAPGQIAIAKLR 244 Query: 244 SVLMIL 249 V+ IL Sbjct: 245 EVMDIL 250 Lambda K H 0.321 0.133 0.368 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: 204 Number of extensions: 1 Number of successful extensions: 1 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: 252 Length of database: 251 Length adjustment: 24 Effective length of query: 228 Effective length of database: 227 Effective search space: 51756 Effective search space used: 51756 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: 46 (22.3 bits)
Align candidate WP_012968942.1 KVAR_RS21480 (3-dehydroquinase)
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.25965.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-82 263.5 0.0 1.3e-82 263.3 0.0 1.0 1 lcl|NCBI__GCF_000025465.1:WP_012968942.1 KVAR_RS21480 3-dehydroquinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025465.1:WP_012968942.1 KVAR_RS21480 3-dehydroquinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 263.3 0.0 1.3e-82 1.3e-82 2 228 .. 19 246 .. 18 247 .. 0.99 Alignments for each domain: == domain 1 score: 263.3 bits; conditional E-value: 1.3e-82 TIGR01093 2 ilvpltakdleealeelekikevgaDivElRvDllkdvsseksveavaeqlsellkdlplilTiRtqke 70 i+vpl k+l e+l +++ + gaDi+E+RvD++ +v + +v+a+ +++ +lk lpl++T+R++ke lcl|NCBI__GCF_000025465.1:WP_012968942.1 19 ICVPLIGKTLDEILGNAHGLVDAGADIIEWRVDHFTQVRDMTQVMAALAEIRGALKALPLLFTFRSKKE 87 9******************************************************************** PP TIGR01093 71 GGkfkgdeeerleelkeaieknlvdlvDiElkleeeavkelikeakkaktkiilSnHdfektpskeelv 139 GG+ + ++e+++++++ea+ ++lvd++DiEl+ +e+++++l+ +a++a++k+i+SnHdf+ktp +e+++ lcl|NCBI__GCF_000025465.1:WP_012968942.1 88 GGETEISDEAYFALNREAARSGLVDVIDIELFNDEAQIRALVDDAHAAGVKVIMSNHDFHKTPAQEDII 156 ********************************************************************* PP TIGR01093 140 erlekaqsldaDivKiavmaksieDvltLleitlkveeek.dkplialsMgekGkisRvlgavlgsvlt 207 rl+++q+l+aD++Kiavm++s +DvltLl++tl ++e++ ++pli++sMg+ G +sRv+g ++gs++t lcl|NCBI__GCF_000025465.1:WP_012968942.1 157 YRLRRMQDLGADLPKIAVMPQSPQDVLTLLAATLTMKEKYaTRPLITMSMGKSGGVSRVTGRLFGSAMT 225 ***************************************9***************************** PP TIGR01093 208 fgslgkasAPGQisvkelrel 228 fg++g+asAPGQi +++lre+ lcl|NCBI__GCF_000025465.1:WP_012968942.1 226 FGTVGQASAPGQIAIAKLREV 246 *******************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (229 nodes) Target sequences: 1 (251 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 9.08 // [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