Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_012385905.1 BIND_RS15105 KR domain-containing protein
Query= reanno::BFirm:BPHYT_RS04775 (263 letters) >NCBI__GCF_000019845.1:WP_012385905.1 Length = 285 Score = 99.0 bits (245), Expect = 1e-25 Identities = 77/258 (29%), Positives = 117/258 (45%), Gaps = 20/258 (7%) Query: 12 GLRVLISGAAAGIGAAIAQAFLDVGANVYICDVDPAAIDRARTAHPQLHAG------VAD 65 G R +I+GA +GIG AIA A+ GA++ + ++ D T AG D Sbjct: 42 GKRAIITGADSGIGRAIAIAYAREGADLVLSYLNEGE-DAEETKSWVAKAGRKAVLVAGD 100 Query: 66 VSDCAQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFL 125 V + I+ A S+LGG+D+L+NNA A+ED+ EWE T NL++ FY + Sbjct: 101 VQYASHCRGIVATAMSELGGIDILVNNAAHQMTFTAIEDILDEEWELTFKVNLHAMFYLV 160 Query: 126 RKAVPLLKETSANPGIIAMASVAGRLGYAFRTPYAASKWAIVGMVKSLAIELGPNNVRVN 185 + AVP + SA II AS+ PYA +K AI LA L +R N Sbjct: 161 KAAVPHMLPGSA---IINTASINADFPNPTLLPYATTKGAIQNFTAGLAQLLADKGIRAN 217 Query: 186 AILPGVVEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLASPA 245 A+ PG + + + A + + + ++R ++A + LA P Sbjct: 218 AVAPGPIWTPLIPSTMPEEAVE----------HFGESVPMKRPGQPAELATAYVMLADPL 267 Query: 246 GQNISGQAISVDGNVEYL 263 +SG I+V G +L Sbjct: 268 SSFVSGATIAVTGGKPFL 285 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: 174 Number of extensions: 6 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: 285 Length adjustment: 25 Effective length of query: 238 Effective length of database: 260 Effective search space: 61880 Effective search space used: 61880 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