Align Gluconolactonase (characterized, see rationale)
to candidate CA265_RS13655 CA265_RS13655 hypothetical protein
Query= uniprot:A0A165IRV8 (316 letters) >FitnessBrowser__Pedo557:CA265_RS13655 Length = 291 Score = 153 bits (387), Expect = 4e-42 Identities = 94/286 (32%), Positives = 149/286 (52%), Gaps = 19/286 (6%) Query: 35 LGEGVLWSVREQAVYWVDILGRELHRWDPATGAHQRWTFDEEISAIAER---AHAPGFIV 91 LGEG W Q ++DI G+ + +PA G ++ISA+ A +V Sbjct: 16 LGEGARWHAGWQKFLFIDIKGKLIGTCNPANGK----VVTKKISAMPGMLAPAENDQLLV 71 Query: 92 TLRRGFALFDPATDMA---PRYLHQPEPDRAGNRFNDGKCDAQGRFWAGSMDFACEAPTG 148 L+ LF+ AT ++ PE NR NDG CDA GR W G+M+ + G Sbjct: 72 ALQGKIVLFNLATGKTINLAKFKEDPE-----NRSNDGACDALGRLWVGTMNINAKHGAG 126 Query: 149 ALYRYDSDGSCTRHDDGFAVTNGPTWSGTGQGAAMFFNATIEGNTYRYDSDLATGTVSNK 208 LY Y+ G + +G +V+NG WS + +++ + + +D DLATG +SN+ Sbjct: 127 NLYCYN--GKLVKKIEGTSVSNGICWSQDNR--TLYYIDSFLYHIKAFDYDLATGNISNE 182 Query: 209 TLWKHWLPEDGLPDGMTTDAQGRLWIAHWGGWCVTCHDPVTAAELGRVRLPVSQVTTCAF 268 + + + DGM D++G LW+A WGG CV ++P+T A +G++ + VT+CAF Sbjct: 183 RIVVEITEPNTVADGMCIDSEGMLWVAIWGGACVNRYNPLTGACIGKIEINAPNVTSCAF 242 Query: 269 GGADLRTLFISSARVGLTPEQLAAEPLAGALFAVDTDSLGLPAHPF 314 GG + + I++A+ GL+ ++L P +G+LF V GLP P+ Sbjct: 243 GGKLMNQMLITTAKDGLSADELKKYPHSGSLFMVKLKVTGLPTAPY 288 Lambda K H 0.321 0.137 0.457 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: 345 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 316 Length of database: 291 Length adjustment: 27 Effective length of query: 289 Effective length of database: 264 Effective search space: 76296 Effective search space used: 76296 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