Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_007473935.1 CMTB2_RS03190 type II 3-dehydroquinate dehydratase
Query= BRENDA::Q48255 (167 letters) >NCBI__GCF_000170735.1:WP_007473935.1 Length = 158 Score = 165 bits (417), Expect = 4e-46 Identities = 83/160 (51%), Positives = 108/160 (67%), Gaps = 2/160 (1%) Query: 1 MKILVIQGPNLNMLGHRDPRLYGMVTLDQIHEIMQTFVKQGNLDVELEFFQTNFEGEIID 60 MKI VI GPNLNMLG R+ +YG + L+ I++ M+ KQ E+EF+Q+N EG+I+D Sbjct: 1 MKIKVIHGPNLNMLGIREVNIYGPMKLEDINKNMEVVAKQNGF--EIEFYQSNHEGDIVD 58 Query: 61 KIQESVGSDYEGIIINPGAFSHTSIAIADAIMLAGKPVIEVHLTNIQAREEFRKNSYTGA 120 IQES+ +GIIINP AF+HTSIAI DAI P +EVHL+NI ARE+FRK S Sbjct: 59 AIQESINEKVDGIIINPAAFTHTSIAIRDAIKAVNLPTVEVHLSNIAAREDFRKKSLISD 118 Query: 121 ACGGVIMGFGPLGYNMALMAMVNILAEMKAFQEAQKNNPN 160 G I GFGP Y++ L+AM+ IL E+K +E Q+N N Sbjct: 119 IVAGTITGFGPFSYHLGLLAMMQILNEIKMLKEQQQNQGN 158 Lambda K H 0.320 0.137 0.392 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: 89 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: 167 Length of database: 158 Length adjustment: 18 Effective length of query: 149 Effective length of database: 140 Effective search space: 20860 Effective search space used: 20860 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: 43 (21.2 bits)
Align candidate WP_007473935.1 CMTB2_RS03190 (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.12282.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-65 202.9 0.5 9.5e-65 202.7 0.5 1.0 1 lcl|NCBI__GCF_000170735.1:WP_007473935.1 CMTB2_RS03190 type II 3-dehydroq Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000170735.1:WP_007473935.1 CMTB2_RS03190 type II 3-dehydroquinate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 202.7 0.5 9.5e-65 9.5e-65 1 140 [. 2 142 .. 2 143 .. 0.98 Alignments for each domain: == domain 1 score: 202.7 bits; conditional E-value: 9.5e-65 TIGR01088 1 kilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeq.vdg 68 ki v++GPnln+LG re+++yG ++le+i++++e ak+++ e+e++qsn+eg+++d+i+e+ ++ vdg lcl|NCBI__GCF_000170735.1:WP_007473935.1 2 KIKVIHGPNLNMLGIREVNIYGPMKLEDINKNMEVVAKQNGFEIEFYQSNHEGDIVDAIQESINEkVDG 70 689**********************************************************98766*** PP TIGR01088 69 ivinpaalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklaleal 137 i+inpaa+thts+a+rDa++av+lP+vevhlsn+ are+frkks+++++ G+i+G+G+ +y+l+l a+ lcl|NCBI__GCF_000170735.1:WP_007473935.1 71 IIINPAAFTHTSIAIRDAIKAVNLPTVEVHLSNIAAREDFRKKSLISDIVAGTITGFGPFSYHLGLLAM 139 ********************************************************************* PP TIGR01088 138 vea 140 +++ lcl|NCBI__GCF_000170735.1:WP_007473935.1 140 MQI 142 987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (141 nodes) Target sequences: 1 (158 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: 4.00 // [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