Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_057507424.1 ABB28_RS04150 type II 3-dehydroquinate dehydratase
Query= BRENDA::Q9PH97 (148 letters) >NCBI__GCF_001431535.1:WP_057507424.1 Length = 147 Score = 216 bits (549), Expect = 2e-61 Identities = 103/146 (70%), Positives = 120/146 (82%) Query: 1 MAHLLLLHGPNLNLLGTREPEIYGRITLPQIDAALAERATAAGHGLSSLQSNAEHVLIER 60 MA LL+LHGPNLNLLGTREP +YG TLPQID AL + AAGH + SLQSNAEHVL++R Sbjct: 1 MAKLLVLHGPNLNLLGTREPGVYGHTTLPQIDQALHAQGAAAGHAVESLQSNAEHVLVDR 60 Query: 61 IHATPEDGTAFILINPGAFTHTSVALRDALLAVALPFVEIHLSNPYTREPFRHHSYLADK 120 I A DGTAFILINP AFTHTSVALRDAL AV +PF+EIHLSNP++REPFR HSY +DK Sbjct: 61 IQAARLDGTAFILINPAAFTHTSVALRDALAAVDVPFIEIHLSNPHSREPFRQHSYFSDK 120 Query: 121 ALGVVCGFGVDSYRIALEGVIARLGS 146 A+GV+CGFG DSYR A++ + RL + Sbjct: 121 AVGVICGFGADSYRYAMDAALQRLSN 146 Lambda K H 0.322 0.139 0.406 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: 109 Number of extensions: 3 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: 148 Length of database: 147 Length adjustment: 16 Effective length of query: 132 Effective length of database: 131 Effective search space: 17292 Effective search space used: 17292 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 WP_057507424.1 ABB28_RS04150 (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.22709.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-57 178.4 0.0 3.3e-57 178.2 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057507424.1 ABB28_RS04150 type II 3-dehydroq Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057507424.1 ABB28_RS04150 type II 3-dehydroquinate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 178.2 0.0 3.3e-57 3.3e-57 1 139 [. 3 142 .. 3 144 .. 0.97 Alignments for each domain: == domain 1 score: 178.2 bits; conditional E-value: 3.3e-57 TIGR01088 1 kilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeq.vdg 68 k+lvl+GPnlnlLG+rep+vyG++tl +i++ l++++++++ ve +qsn e l+d+i+ a + + lcl|NCBI__GCF_001431535.1:WP_057507424.1 3 KLLVLHGPNLNLLGTREPGVYGHTTLPQIDQALHAQGAAAGHAVESLQSNAEHVLVDRIQAARLDgTAF 71 689*********************************************************99765599* PP TIGR01088 69 ivinpaalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklaleal 137 i+inpaa+thtsvalrDalaav +P++e+hlsn h re+fr++s++++ a Gvi+G+Ga +y+ a+ a+ lcl|NCBI__GCF_001431535.1:WP_057507424.1 72 ILINPAAFTHTSVALRDALAAVDVPFIEIHLSNPHSREPFRQHSYFSDKAVGVICGFGADSYRYAMDAA 140 ******************************************************************998 PP TIGR01088 138 ve 139 ++ lcl|NCBI__GCF_001431535.1:WP_057507424.1 141 LQ 142 76 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (141 nodes) Target sequences: 1 (147 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: 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