Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_077276299.1 BW732_RS08225 SDR family oxidoreductase
Query= reanno::BFirm:BPHYT_RS04775 (263 letters) >NCBI__GCF_001998885.1:WP_077276299.1 Length = 259 Score = 117 bits (293), Expect = 2e-31 Identities = 85/252 (33%), Positives = 129/252 (51%), Gaps = 12/252 (4%) Query: 14 RVLISGAAAGIGAAIAQAFLDVGANVYICDVDPAAID----RARTAHPQLHAGVADVSDC 69 RV+I+GA +GIG A A F ++GA V + D++ +D + + + V DV D Sbjct: 8 RVVITGAGSGIGRATALKFAELGAVVGLIDINEQGLDDIVKEIYRHNGEAYYEVVDVMDE 67 Query: 70 AQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRKAV 129 ++ I ++LGGLD L+ NAGI G +E L +W RTI TNL S F L+ A+ Sbjct: 68 ERLMEGIAQLANQLGGLDGLVCNAGINGTWAPIETLKIEDWHRTIDTNLTSTFVSLKAAI 127 Query: 130 PLLKETSANPGIIAMASVAGRLGY--AFRTPYAASKWAIVGMVKSLAIELGPNNVRVNAI 187 PL+K+ + I+ +S+ G Y + Y+ SK V ++K A+EL N+RVNA+ Sbjct: 128 PLMKDDGGS--IVITSSINGNRIYNNFGASAYSTSKAGQVSLMKMAALELARCNIRVNAV 185 Query: 188 LPGVVEGE-RMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLASPAG 246 PG +E +I E + I + +G+ K + V +V A FL S Sbjct: 186 CPGAIETPINSKTIIEKETEEVQIKVEFPEGDRPLKADTGQPEQVANVIA---FLISSQS 242 Query: 247 QNISGQAISVDG 258 N+SG + VDG Sbjct: 243 GNVSGTEVYVDG 254 Lambda K H 0.320 0.136 0.391 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: 146 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: 263 Length of database: 259 Length adjustment: 25 Effective length of query: 238 Effective length of database: 234 Effective search space: 55692 Effective search space used: 55692 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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