Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate Ac3H11_29 3-dehydroquinate dehydratase II (EC 4.2.1.10)
Query= BRENDA::A0A124C1Y7 (157 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_29 Length = 158 Score = 164 bits (415), Expect = 6e-46 Identities = 80/152 (52%), Positives = 105/152 (69%), Gaps = 6/152 (3%) Query: 6 ANAPIMILNGPNLNLLGQRQPEIYGSDTLADVEALCVKAAATHGGTVDFRQSNHEGELVD 65 A+ + +LNGPNLNLLG R+P +YG+ TLADVE LC +A HG + F QSNHEG LVD Sbjct: 3 AHKTVFVLNGPNLNLLGTREPAVYGAQTLADVEKLCAEACQRHGYALRFHQSNHEGALVD 62 Query: 66 WIHEARMDH-----CGIVINPGAYSHTSVAILDALNTCDGLPVIEVHISNIHKREAFRHH 120 WIHEA H G+VIN GAY+HTS+A+ DA+ G+ +IE+HISN+H REA+RHH Sbjct: 63 WIHEAGRLHAAGELAGVVINAGAYTHTSIALHDAIKG-TGITLIELHISNVHAREAYRHH 121 Query: 121 SYVSLRADGVIAGCGVQGYVFGVERVAALAGE 152 SY++ A V+ G GV GY ++ +A L + Sbjct: 122 SYMAAAAKAVMCGFGVLGYGLAIDGLAQLLAQ 153 Lambda K H 0.321 0.137 0.416 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: 122 Number of extensions: 4 Number of successful extensions: 3 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: 157 Length of database: 158 Length adjustment: 17 Effective length of query: 140 Effective length of database: 141 Effective search space: 19740 Effective search space used: 19740 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 Ac3H11_29 (3-dehydroquinate dehydratase II (EC 4.2.1.10))
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.17848.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.6e-56 173.5 0.2 1.1e-55 173.2 0.2 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_29 3-dehydroquinate dehydratase II Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_29 3-dehydroquinate dehydratase II (EC 4.2.1.10) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 173.2 0.2 1.1e-55 1.1e-55 2 139 .. 7 149 .. 6 151 .. 0.95 Alignments for each domain: == domain 1 score: 173.2 bits; conditional E-value: 1.1e-55 TIGR01088 2 ilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihea... 62 + vlnGPnlnlLG+rep+vyG++tl ++e+l+ ea ++++ + + qsn+eg l+d+ihea lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_29 7 VFVLNGPNLNLLGTREPAVYGAQTLADVEKLCAEACQRHGYALRFHQSNHEGALVDWIHEAgrl 70 78*********************************************************96333 PP TIGR01088 63 ..leqvdgivinpaalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivG 124 ++++ g+vin++a+thts+al Da++ + ++e+h+snvhare +r++s++a++ak v++G lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_29 71 haAGELAGVVINAGAYTHTSIALHDAIKGTGITLIELHISNVHAREAYRHHSYMAAAAKAVMCG 134 3368899********************************************************* PP TIGR01088 125 lGakgyklalealve 139 +G+ gy la+ l++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_29 135 FGVLGYGLAIDGLAQ 149 **********98876 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: 4.17 // [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