Align galactaro-1,5-lactonase (characterized)
to candidate RR42_RS30140 RR42_RS30140 gluconolaconase
Query= reanno::WCS417:GFF3393 (291 letters) >FitnessBrowser__Cup4G11:RR42_RS30140 Length = 292 Score = 154 bits (388), Expect = 3e-42 Identities = 103/279 (36%), Positives = 143/279 (51%), Gaps = 14/279 (5%) Query: 13 VGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIARTDAGNWVAGMET 72 +GE PVW G +A+Y+VDI + R++ ATG + +W I D G ++ GM+ Sbjct: 16 LGEGPVWHQGSSAVYFVDIKGRRIHRFAIATGAMRSWPVDSQPGFIVPLDDGGFLCGMQD 75 Query: 73 GFFQLTPHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVLNMGLNAAEGTLY 132 G ++ P DG+ L VE R+NDG D GR W G+M + G A G+LY Sbjct: 76 GLYRFDPA-DGACRR--LKEVEPDLPGNRINDGFVDPAGRLWFGTM--DDGEAAPSGSLY 130 Query: 133 RYTSGAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFDYDIDTGTPSNRRVF 192 + + G++ NG A SPD RT+Y +D+ + + ++AFD D G S RR F Sbjct: 131 QVGDDGRTWRRDSGYVITNGPAMSPDARTLYHADT--VKRLVYAFDVGQD-GALSRRREF 187 Query: 193 VDMHKHLGRPDGAAVDADGCYWICANDAGLIHRFSPDGRLDRSLTVPVKKPTMCAFGGSR 252 + G PDG AVDADG WI I R+SPDGRL + P T AFGG Sbjct: 188 ARLCG-TGYPDGMAVDADGHLWIAVFGGARIERWSPDGRLAGVVRFPCDNVTKLAFGGDD 246 Query: 253 LDTLFVTSIRDDQSE-----QSLSGGVFALNPGVVGLPE 286 L T++VT+ R S Q L+GG+F+ GLP+ Sbjct: 247 LRTVYVTTARKGLSPAALALQPLAGGLFSFRAPTRGLPQ 285 Lambda K H 0.321 0.137 0.443 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: 404 Number of extensions: 32 Number of successful extensions: 5 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: 291 Length of database: 292 Length adjustment: 26 Effective length of query: 265 Effective length of database: 266 Effective search space: 70490 Effective search space used: 70490 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: 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