Align 3-dehydroquinate synthase; DHQ synthase; 3-dehydroquinate synthase II; EC 1.4.1.24 (characterized)
to candidate WP_011033219.1 MM_RS06580 3-dehydroquinate synthase II
Query= SwissProt::Q58646 (361 letters) >NCBI__GCF_000007065.1:WP_011033219.1 Length = 380 Score = 341 bits (874), Expect = 2e-98 Identities = 186/377 (49%), Positives = 247/377 (65%), Gaps = 23/377 (6%) Query: 5 WVNVIGDNWEEKKKIVTTALESSIPVVVAEPEDIEKIKELGNIKVASHSLD----ADIVL 60 W+ WEE+K+ +TT LES V+ P D+EK++ELGNI VA+ + D ADIV+ Sbjct: 7 WIKADEGGWEEQKERITTGLESGADCVLVNPGDVEKVRELGNITVAAFARDNKSGADIVV 66 Query: 61 VNKNDNIEFLKEAK----------------NLGKETAIYIPIESKEDEEFASEVARFGFV 104 V K + K + G Y+ I+ + E FA+E+ + Sbjct: 67 VGKRGEGDGTKPLPQEIPGSFDVNAATLLTDKGVTVGGYVVIKDRSYERFAAEMGKI--C 124 Query: 105 DNIILEGRDWTIIPLENLIADLFHRDVKIVASVNSVDEAKVAYEILEKGTDGVLLNPKNL 164 D +++ G DW +IPLENLIADL VKI+ V S +EA++A++ LE G DGVLL+ N Sbjct: 125 DYLLVTGTDWKVIPLENLIADLQREKVKIIFGVKSAEEARLAFQTLETGADGVLLDSGNP 184 Query: 165 EDIKELSKLIEEMNKEKVALDVATVTKVEPIGSGDRVCIDTCSLMKIGEGMLIGSYSRAL 224 ++IK+ K E+ E L+ A VT+VEP+G GDRVC+DTC+LM+ GEGMLIGS + + Sbjct: 185 QEIKDTIKAARELESESTELESAVVTRVEPLGMGDRVCVDTCNLMQRGEGMLIGSQASGM 244 Query: 225 FLVHSETVENPYVATRPFRVNAGPVHAYILCPGNKTKYLSELKAGDKVLIVDKDGNTREA 284 FLV+SE+ ++PYVA RPFRVNAG VH+YI G+KT+YLSEL+AGD V I+D G RE Sbjct: 245 FLVNSESDDSPYVAARPFRVNAGAVHSYIKI-GDKTRYLSELQAGDSVTIIDSRGKQREG 303 Query: 285 IVGRVKIERRPLVLIEAEYKGDIIRTILQNAETIRLVNEKGEPISVVDLKPGDKVLIKPE 344 IVGR+KIE RPL+LIEA+ + ILQNAETI+LV + G PISV LK GD+VL++ E Sbjct: 304 IVGRIKIESRPLMLIEAKAGDRTLTAILQNAETIKLVGKGGTPISVAKLKKGDEVLVRLE 363 Query: 345 EYARHFGMAIKETIIEK 361 E ARHFG I+ETIIEK Sbjct: 364 EGARHFGKKIEETIIEK 380 Lambda K H 0.315 0.136 0.380 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: 472 Number of extensions: 29 Number of successful extensions: 4 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: 361 Length of database: 380 Length adjustment: 30 Effective length of query: 331 Effective length of database: 350 Effective search space: 115850 Effective search space used: 115850 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: 42 (22.0 bits) S2: 49 (23.5 bits)
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