Align 2-deoxy-3-keto-D-ribonoate cleavage enzyme (characterized)
to candidate WP_086508578.1 BZY95_RS03370 3-keto-5-aminohexanoate cleavage protein
Query= reanno::WCS417:GFF1426 (310 letters) >NCBI__GCF_002151265.1:WP_086508578.1 Length = 276 Score = 126 bits (317), Expect = 5e-34 Identities = 90/298 (30%), Positives = 139/298 (46%), Gaps = 29/298 (9%) Query: 6 PVIITCAVTGAIHTPSMSPHLPITAQEIADAAIGAAEAGAAIVHLHARDPNDGRPSQDPA 65 P II A+TG++ +P +PIT +E ++ A EAGA I H H R+ +D P+ DP Sbjct: 4 PCIICVAITGSLPRKENNPAVPITIEEQIESTQAAFEAGATIAHCHVRN-DDQTPTSDPE 62 Query: 66 LFAEFLPQIKA-ASDVVINITTGGAPTMGVEERLQPVMQFKPELASLNMGSMNFGLYEML 124 FA + +K ++I ++TGG G E ++ KP++ASL++GS NF Sbjct: 63 KFARLMEGLKKHCPGMIIQLSTGGRSGAGKERG--GMLPLKPDMASLSVGSNNF------ 114 Query: 125 NRFTDFKHDWERPYLEESDDRIFRNTFRDITHILNACAENRTRFEIECYDIGHLYTAAHF 184 +R++ N+ + + + + + EIE +D+ H++ A Sbjct: 115 ------------------PNRVYENSPQLVEWLAEEMLQYAIKPEIEAFDLSHIHQAVAL 156 Query: 185 LERGLLKPPLFIQSVFGLRGGIGGHPEDLAHMRRTADRLFGSDYVWSILGAGRGQIPLAT 244 G LK PL++Q V G++ + T RL D W G G Q L Sbjct: 157 SREGKLKAPLYVQFVMGVKNAMPADKPTFDIYIETLKRL-APDAQWCGAGIGPNQYLLNE 215 Query: 245 MGLSMGSNARVGLEDSLWDGPGKLAASNADQVRRIRTVIEALGHRVATPDEAREILGL 302 ++ G + R GLED++ LA SNA V R + E +AT +AREILGL Sbjct: 216 WSIAAGGHTRTGLEDNVRLDRDTLAPSNAALVERAVALCEKYERPIATWQQAREILGL 273 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: 241 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: 276 Length adjustment: 26 Effective length of query: 284 Effective length of database: 250 Effective search space: 71000 Effective search space used: 71000 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 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