Align 2-deoxy-3-keto-D-ribonoate cleavage enzyme (characterized)
to candidate 3610094 Dshi_3475 protein of unknown function DUF849 (RefSeq)
Query= reanno::WCS417:GFF1426 (310 letters) >FitnessBrowser__Dino:3610094 Length = 279 Score = 122 bits (306), Expect = 1e-32 Identities = 94/301 (31%), Positives = 145/301 (48%), Gaps = 31/301 (10%) Query: 5 RPVIITCAVTGAIHTPSMSPHLPITAQEIADAAIGAAEAGAAIVHLHARDPNDGRPSQDP 64 +P II A+TG++ T S +P +PIT E ++ A EAGA+I H H R+ +D PS DP Sbjct: 4 KPCIICVAITGSVATKSANPAVPITVAEQVESTHEAFEAGASICHAHVRN-DDETPSSDP 62 Query: 65 ALFAEFLPQI-KAASDVVINITTGGAPTMGVEERLQPVMQFKPELASLNMGSMNFGLYEM 123 FA + K ++I +TGG G E ++ +P++ASL +GS NF Sbjct: 63 EKFARLQEGLQKHCPGMIIQFSTGGRSGAGRER--GGMLPLRPDMASLTVGSNNF----- 115 Query: 124 LNRFTDFKHDWERPYLEESDDRIFRNTFRDITHILNACAENRTRFEIECYDIGHLYTAAH 183 R++ N + + + + EIE +D+ H++ AA Sbjct: 116 -------------------PTRVYENPPDLVDWLASEMRAHEVIPEIEAFDLSHIHHAAL 156 Query: 184 FLERGLLKPPLFIQSVFGLRGGIGGHPEDLAHMRRTADRLF-GSDYVWSILGAGRGQIPL 242 G L +IQ V G++ + E R T +RL G+++ + +GA QI + Sbjct: 157 MHRDGRLATRPYIQFVMGVKNAMPVDRETFDFYRATVERLLPGAEWCGAAIGA--SQIVM 214 Query: 243 ATMGLSMGSNARVGLEDSLWDGPGKLAASNADQVRRIRTVIEALGHRVATPDEAREILGL 302 ++ G +AR GLED++ LA SNA VRR+ + VA P +AREILGL Sbjct: 215 NEWCVAEGGHARTGLEDNVRLDRETLAPSNAALVRRVVELCNQYERPVADPAQAREILGL 274 Query: 303 K 303 + Sbjct: 275 R 275 Lambda K H 0.321 0.138 0.416 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: 239 Number of extensions: 14 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: 310 Length of database: 279 Length adjustment: 26 Effective length of query: 284 Effective length of database: 253 Effective search space: 71852 Effective search space used: 71852 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 (21.9 bits) S2: 48 (23.1 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