Align 2-deoxy-3-keto-D-ribonoate cleavage enzyme (characterized)
to candidate AZOBR_RS23055 AZOBR_RS23055 hypothetical protein
Query= reanno::WCS417:GFF1426 (310 letters) >FitnessBrowser__azobra:AZOBR_RS23055 Length = 314 Score = 443 bits (1139), Expect = e-129 Identities = 210/306 (68%), Positives = 246/306 (80%) Query: 5 RPVIITCAVTGAIHTPSMSPHLPITAQEIADAAIGAAEAGAAIVHLHARDPNDGRPSQDP 64 R VIITCAVTG+IHTPSMSPHLP+T +IA AI A EAGAAIVHLHARDP GRP+QDP Sbjct: 9 RKVIITCAVTGSIHTPSMSPHLPVTPDQIAAEAIAAVEAGAAIVHLHARDPETGRPTQDP 68 Query: 65 ALFAEFLPQIKAASDVVINITTGGAPTMGVEERLQPVMQFKPELASLNMGSMNFGLYEML 124 LF FLP+IK A+ V+NITTGG+ M VE+RL+P QF+PE+ASLNMGSMNFGL+ ML Sbjct: 69 DLFQRFLPRIKQATKAVVNITTGGSAAMTVEDRLRPAAQFQPEVASLNMGSMNFGLFPML 128 Query: 125 NRFTDFKHDWERPYLEESDDRIFRNTFRDITHILNACAENRTRFEIECYDIGHLYTAAHF 184 NRF+ F+HDWER YLE S D +F+NTF+DI HIL C+ N TRFE ECYDI HLYT AHF Sbjct: 129 NRFSAFQHDWERTYLENSRDLVFKNTFKDIEHILKTCSGNGTRFEFECYDISHLYTLAHF 188 Query: 185 LERGLLKPPLFIQSVFGLRGGIGGHPEDLAHMRRTADRLFGSDYVWSILGAGRGQIPLAT 244 L+R L+ PPLF+QSVFG+ GGIG HPED+ HM+RTADRLFG YVWS+LGAGR Q+P+AT Sbjct: 189 LDRKLVTPPLFVQSVFGILGGIGPHPEDVMHMKRTADRLFGDQYVWSVLGAGRNQMPIAT 248 Query: 245 MGLSMGSNARVGLEDSLWDGPGKLAASNADQVRRIRTVIEALGHRVATPDEAREILGLKG 304 L++G N RVGLED+LW GPG+LA SNA+QV +R +IE L VATPDEAR +L LKG Sbjct: 249 QSLALGGNVRVGLEDNLWAGPGRLATSNAEQVAMVRKLIEGLALEVATPDEARAMLSLKG 308 Query: 305 RDQVNF 310 D V F Sbjct: 309 GDAVTF 314 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: 343 Number of extensions: 8 Number of successful extensions: 1 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: 314 Length adjustment: 27 Effective length of query: 283 Effective length of database: 287 Effective search space: 81221 Effective search space used: 81221 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 Apr 09 2024. 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