Align prephenate and/or arogenate dehydrogenase (characterized)
to candidate 8501010 DvMF_1747 Prephenate dehydrogenase (RefSeq)
Query= reanno::DvH:209400 (255 letters) >FitnessBrowser__Miya:8501010 Length = 263 Score = 358 bits (918), Expect = e-104 Identities = 184/258 (71%), Positives = 208/258 (80%), Gaps = 4/258 (1%) Query: 1 MKIALVGDKGRMGRLLTSRFSAAGCEVAGVDRPLTPDTVRPAVQGADVVILCVPVEVLAE 60 +KIALVG GRMGRL R SAAG V GVDRPLT D +R AV GA V+LCVPVEV+ E Sbjct: 4 VKIALVGAGGRMGRLFADRLSAAGYAVGGVDRPLTQDVLRHAVDGAAAVLLCVPVEVMDE 63 Query: 61 VLSIVAPLLSPKQVLADITSVKVRPMEVMQAFHAGPVVGTHPLFGPDPQD----DHLPVA 116 VL VAPLL+ QVLADITSVKVRPM+VM+ +AGPVVGTHPLFGP P ++L VA Sbjct: 64 VLRQVAPLLNGMQVLADITSVKVRPMQVMERHYAGPVVGTHPLFGPVPPAGDPAENLRVA 123 Query: 117 VTPGSSARDADVTLVEQCFRMIGCDTFRTTAQEHDRAAAMIQGLNFISSVAYLATLAHNE 176 VTPG +A + DV L+E+ F +GC FRTTA EHD AAA IQGLNFI+SVAYLATLAH + Sbjct: 124 VTPGDTAHETDVALIERVFADMGCVPFRTTADEHDEAAACIQGLNFITSVAYLATLAHRD 183 Query: 177 ELLPFVTPSFRRRLDAARKMLTEDAALFEGMFEANPASQDAVRSFRSFLNIASAGDVDVL 236 EL PF+TPSFRRRLDAARKMLTEDA+LFEGMFEANP SQ AVRS+ SFLN A+AGDVDVL Sbjct: 184 ELTPFITPSFRRRLDAARKMLTEDASLFEGMFEANPHSQTAVRSYLSFLNFAAAGDVDVL 243 Query: 237 VDRARWWWRTHDDRGGAR 254 VDRA+WWWR+H +RGG R Sbjct: 244 VDRAQWWWRSHTERGGVR 261 Lambda K H 0.323 0.136 0.407 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: 300 Number of extensions: 6 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: 255 Length of database: 263 Length adjustment: 24 Effective length of query: 231 Effective length of database: 239 Effective search space: 55209 Effective search space used: 55209 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 (22.0 bits) S2: 47 (22.7 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