Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate 3610403 Dshi_3784 Gluconate 2-dehydrogenase (acceptor) (RefSeq)
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__Dino:3610403 Length = 305 Score = 164 bits (415), Expect = 4e-45 Identities = 94/258 (36%), Positives = 131/258 (50%), Gaps = 10/258 (3%) Query: 50 VSRGEYVARLSDCVACHSL--AGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLAD 107 V RG Y+AR S C+ACH+ AG AP AGG + TP G + N+T D G+G ++ Sbjct: 40 VDRGAYLARASGCIACHTNFEAGGAPLAGGAPLETPFGTFYPPNLTTDPEHGMGEWTAEQ 99 Query: 108 FDRAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPL 167 F +AVR G+ P G YP+ PY Y SD DI L+A F Q + P ++P +D+ +P Sbjct: 100 FAKAVRQGIGPDGTPYYPSFPYTFYADFSDQDIADLWAAF-QTVPPVDEPAPENDVSFPF 158 Query: 168 NMRWPIALWNGVFAPTATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDE 227 + RW + LW F + WNRG +V+G HCG+CHTPR LA + Sbjct: 159 DQRWGLKLWRAAFFYDPDTEPIEGRSDAWNRGRELVRGAAHCGACHTPRNLAGGR----D 214 Query: 228 AGAPFLAGALLDGW-YAPSLRQDPNTGLGRWSEPQIVQFLKTGRNAHAVVY-GSMTEAFN 285 GA F A L G AP++R + W+ + L+TG + GSM E Sbjct: 215 IGASFAGNAQLPGGSKAPAIR-PKDLVKNDWTVSNLAYALQTGITPSGDAFGGSMAEVVR 273 Query: 286 NSTQFMQDDDLAAIARYL 303 T+F+ D A+A +L Sbjct: 274 EGTRFLTPADREAMALFL 291 Lambda K H 0.318 0.133 0.423 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: 442 Number of extensions: 31 Number of successful extensions: 6 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: 447 Length of database: 305 Length adjustment: 30 Effective length of query: 417 Effective length of database: 275 Effective search space: 114675 Effective search space used: 114675 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: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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