Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate BWI76_RS15085 BWI76_RS15085 3-deoxy-D-arabinose-heptulosonic-7-phosphate synthase
Query= BRENDA::G3XCJ9 (405 letters) >FitnessBrowser__Koxy:BWI76_RS15085 Length = 389 Score = 285 bits (728), Expect = 2e-81 Identities = 159/377 (42%), Positives = 217/377 (57%), Gaps = 9/377 (2%) Query: 15 QQPEWGDPSRLRDVQAYLRGSPALIRAGDILALRATLARVARGEALVVQCGDCAEDMDDH 74 QQP W D L V + L P L+ +I LA V G+A++ Q GDCAE + + Sbjct: 12 QQPFWSDKDMLALVISELDTLPELLSFEEISEFNKALAAVYAGKAMIFQAGDCAERICES 71 Query: 75 HAENVARKAAVLELLAGALRLAGRRPVIRVGRIAGQYAKPRSKPHEQVGEQTLPVYRGDM 134 A +V +K LE ++ L P++ VGRIAGQYAKPRS+ +E G++ LPV+RGD Sbjct: 72 DALHVRKKLTFLEQMSRELSTLMGLPILTVGRIAGQYAKPRSQHNEVDGDRVLPVWRGDS 131 Query: 135 VNGREAHAEQRRADPQRILKGY-AAARNIMRHLGWDAASGQEANASPVWTSHEMLLLDYE 193 VN EA E RR DPQR+L Y AAA + ++ ++ + P+WTSHE LLLDYE Sbjct: 132 VNRPEATPEARRNDPQRMLLSYHAAAETLAEIKRYEREYPRDVH--PIWTSHEALLLDYE 189 Query: 194 LSMLREDEQRRVYLGSTHWPWIGERTRQVDGAHVALLAEVLNPVACKVGPEIGRDQLLAL 253 + +R + YL STHWPWIG RT D H+A+LA + NPVACK+ + + L Sbjct: 190 TTQIRTNPHGESYLASTHWPWIGIRTLAPDSPHIAMLANIANPVACKIDATVTPSFIATL 249 Query: 254 CERLDPRREPGRLTLIARMGAQKVGERLPPLVEAVRAAGHPVIWLSDPMHGNTIVAPCGN 313 C +L+P+R PGRLT I+R G + RL L++A +A PV+W+ DPMHGNT GN Sbjct: 250 CRQLNPQRIPGRLTFISRFGRSHI-HRLGALIQAAQATETPVLWMCDPMHGNTGKTQAGN 308 Query: 314 KTRLVRSIAEEVAAFRLAVSGSGGVAAGLHLETTPDDVTECVADSS--GLHQVSRHYTSL 371 K R + + E++ F V AAGLHLE TP+ V EC +++ H++ + L Sbjct: 309 KRRELSDMMAEISGFLRQVKSHNACAAGLHLEATPNPVIECFCENNHPEEHELKQ---IL 365 Query: 372 CDPRLNPWQALSAVMAW 388 CDPRLN Q + W Sbjct: 366 CDPRLNVAQTQMLLTHW 382 Lambda K H 0.320 0.134 0.410 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: 432 Number of extensions: 28 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: 405 Length of database: 389 Length adjustment: 31 Effective length of query: 374 Effective length of database: 358 Effective search space: 133892 Effective search space used: 133892 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: 50 (23.9 bits)
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