Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_013430006.1 CALKRO_RS05120 type II 3-dehydroquinate dehydratase
Query= BRENDA::G8M0G7 (142 letters) >NCBI__GCF_000166775.1:WP_013430006.1 Length = 145 Score = 193 bits (490), Expect = 1e-54 Identities = 93/139 (66%), Positives = 111/139 (79%), Gaps = 1/139 (0%) Query: 1 MKKILIINGPNLNLLGTREKEVYGTETLDDIAKKVAEEAAKLNVNIEFFQSNHEGDIIDK 60 MKK+L+INGPNLNLLG REK +YG+ + +D+ K ++++A +L +EFFQSNHEG+IIDK Sbjct: 1 MKKVLVINGPNLNLLGIREKNIYGSVSYEDVLKSISQKAQELGFEVEFFQSNHEGEIIDK 60 Query: 61 IHAAR-GNTDAIIINPGAYTHYSIAIRDAIKAVEIPTIEIHLSNIHAREEFRSHSVIAPV 119 IH+A DAIIINPGAYTHYS AI DAIKAV IP IE+H+SNIHAREEFR SVIAP Sbjct: 61 IHSAYFEKVDAIIINPGAYTHYSYAIHDAIKAVNIPAIEVHISNIHAREEFRRKSVIAPA 120 Query: 120 CVGQICGFGSNSYILGLNA 138 C GQI GFG SYI+ L A Sbjct: 121 CTGQISGFGIKSYIIALYA 139 Lambda K H 0.319 0.137 0.387 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: 111 Number of extensions: 5 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: 142 Length of database: 145 Length adjustment: 16 Effective length of query: 126 Effective length of database: 129 Effective search space: 16254 Effective search space used: 16254 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 (21.7 bits) S2: 42 (20.8 bits)
Align candidate WP_013430006.1 CALKRO_RS05120 (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.3528250.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-67 209.2 0.7 1e-66 209.1 0.7 1.0 1 NCBI__GCF_000166775.1:WP_013430006.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_013430006.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 209.1 0.7 1e-66 1e-66 1 140 [. 3 143 .. 3 144 .. 0.97 Alignments for each domain: == domain 1 score: 209.1 bits; conditional E-value: 1e-66 TIGR01088 1 kilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihea.leqvdgivin 72 k+lv+nGPnlnlLG re+++yGs+++e++ + ++++a+el+ eve+fqsn+ege+idkih+a +e+vd+i+in NCBI__GCF_000166775.1:WP_013430006.1 3 KVLVINGPNLNLLGIREKNIYGSVSYEDVLKSISQKAQELGFEVEFFQSNHEGEIIDKIHSAyFEKVDAIIIN 75 79**********************************************************984578******* PP TIGR01088 73 paalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalealvea 140 p+a+th+s+a+ Da++av++P +evh+sn+hareefr+ksv+a++++G+i+G+G+k+y +al al e+ NCBI__GCF_000166775.1:WP_013430006.1 76 PGAYTHYSYAIHDAIKAVNIPAIEVHISNIHAREEFRRKSVIAPACTGQISGFGIKSYIIALYALKEI 143 **************************************************************999886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (141 nodes) Target sequences: 1 (145 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: 12.30 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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