Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate CA265_RS09515 CA265_RS09515 type II 3-dehydroquinate dehydratase
Query= BRENDA::E4RLB7 (148 letters) >FitnessBrowser__Pedo557:CA265_RS09515 Length = 139 Score = 151 bits (381), Expect = 4e-42 Identities = 76/139 (54%), Positives = 98/139 (70%), Gaps = 2/139 (1%) Query: 1 MQKVAVIHGPNLNMLGLREPEIYGKNNLEMVNKNLKRKAKELDFEIEIMQSNHEGEIVDY 60 M K+ +I+GPNLN+LG+REP IYG ++E K LK D EIE QSN EGEI++ Sbjct: 1 MMKIQIINGPNLNLLGVREPSIYGNTSIEDYIKELKTVYP--DIEIEYYQSNVEGEIINK 58 Query: 61 LHQNFEQLDGVIINPGGLTHTSVILRDALAAVRLPVIEVHISNIHKREEFRHKSLTAAVA 120 LH+ DGV++N GG THTSV + DA+AA++ PV+EVHISNI+ REE+RH SLT Sbjct: 59 LHEVGFSYDGVVLNAGGYTHTSVAIADAIAAIKTPVVEVHISNIYAREEYRHVSLTGKNC 118 Query: 121 VGQITGLGVKGYTLALEGL 139 G +TG G+KGY LA+E L Sbjct: 119 QGVLTGFGMKGYRLAIESL 137 Lambda K H 0.318 0.138 0.382 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: 113 Number of extensions: 4 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: 148 Length of database: 139 Length adjustment: 16 Effective length of query: 132 Effective length of database: 123 Effective search space: 16236 Effective search space used: 16236 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 42 (20.8 bits)
Align candidate CA265_RS09515 CA265_RS09515 (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.10859.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-58 180.3 0.4 8.1e-58 180.2 0.4 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS09515 CA265_RS09515 type II 3-dehydroq Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS09515 CA265_RS09515 type II 3-dehydroquinate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 180.2 0.4 8.1e-58 8.1e-58 1 137 [. 3 137 .. 3 139 .] 0.96 Alignments for each domain: == domain 1 score: 180.2 bits; conditional E-value: 8.1e-58 TIGR01088 1 kilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeqvdg 68 ki ++nGPnlnlLG rep++yG++++e+ + l++ ++e+e++qsn ege+i+k+he+ ++dg lcl|FitnessBrowser__Pedo557:CA265_RS09515 3 KIQIINGPNLNLLGVREPSIYGNTSIEDYIKELKTVY--PDIEIEYYQSNVEGEIINKLHEVGFSYDG 68 689*************************999998765..679999*********************** PP TIGR01088 69 ivinpaalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalea 136 +v+n++++thtsva++Da+aa++ Pvvevh+sn++aree+r+ s++++ ++Gv++G+G+kgy+la+e lcl|FitnessBrowser__Pedo557:CA265_RS09515 69 VVLNAGGYTHTSVAIADAIAAIKTPVVEVHISNIYAREEYRHVSLTGKNCQGVLTGFGMKGYRLAIES 136 *****************************************************************997 PP TIGR01088 137 l 137 l lcl|FitnessBrowser__Pedo557:CA265_RS09515 137 L 137 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (141 nodes) Target sequences: 1 (139 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: 5.06 // [ok]
This GapMind analysis is from Apr 09 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