Align L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401) (characterized)
to candidate RR42_RS24170 RR42_RS24170 hypothetical protein
Query= metacyc::MONOMER-16233 (285 letters) >FitnessBrowser__Cup4G11:RR42_RS24170 Length = 285 Score = 140 bits (354), Expect = 2e-38 Identities = 92/269 (34%), Positives = 140/269 (52%), Gaps = 39/269 (14%) Query: 20 DGKIRDLSGVVPELTIEALAAAKGADVASLPLVEGEPRYGVPVKGIGKIVAIGLNYEDHA 79 D I + V P + EA+ + + +AS+ R PV GKI+A +NY+DH Sbjct: 40 DWIINNFESVRPHID-EAIESGRRVPLASV-------RLRAPVANPGKIIAAPINYKDHI 91 Query: 80 IESNLPIPTEPMM--------------FMKALSSLNGPNDEVVLPKNSTHGDWEVELGVV 125 E+N +P + F+KA SS+ G ++++ +P D EVEL VV Sbjct: 92 AEAN----NDPQINHGKTFTDLSTLGVFLKANSSVIGCHEDIRIPFPDRRTDHEVELAVV 147 Query: 126 IGETCRFVSEDEALSKVAGYVLVNDVSERFNQKQRGTQWSKGKGHDTFCPVGPWLVTPDE 185 IG + VS + AL+ V GY + D++ R + K DTF +GPW+VT DE Sbjct: 148 IGREAKKVSRENALAFVFGYCIGLDMTVRGPELP-----DFRKSADTFSVLGPWIVTADE 202 Query: 186 VGDPQDLDMHLNVNGTRMQTGNTKTMIFNVAQLISYVSEYITLYPGDLMITGTPPGVGEG 245 + +P LD+ ++VNG Q NTK +I++V +LI Y S TLYPGD+++TGTP GV Sbjct: 203 IPEPNSLDLSIHVNGELRQQSNTKYLIYDVQRLIEYASAMYTLYPGDVIMTGTPAGVSP- 261 Query: 246 KKPQAIYLKAGDVMELGIEKLGTQRQQVS 274 + GD++E + +GT +V+ Sbjct: 262 -------VTYGDILEASVSGIGTMTARVA 283 Lambda K H 0.316 0.137 0.411 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: 205 Number of extensions: 7 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: 285 Length of database: 285 Length adjustment: 26 Effective length of query: 259 Effective length of database: 259 Effective search space: 67081 Effective search space used: 67081 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 47 (22.7 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