Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate WP_010632160.1 RH97_RS09630 SDR family oxidoreductase
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >NCBI__GCF_000246965.1:WP_010632160.1 Length = 299 Score = 139 bits (350), Expect = 7e-38 Identities = 85/256 (33%), Positives = 141/256 (55%), Gaps = 12/256 (4%) Query: 3 LKDKVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEALGR 62 +K++V I++GG GIGRA+AVA A EGAD+ + Y+ +++ + + AV E LG+ Sbjct: 53 MKNQVAIISGGDSGIGRAVAVAFAKEGADLVLAYFDEHEDARETKQAV-------EQLGQ 105 Query: 63 RVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGI-CPFHAFLDMPPEVLESTVAVN 121 R + + G++ +E + ++ T+E FG++D+L +N + + F+D+ E T N Sbjct: 106 RCLLLPGDLRNKEHCKYVISSTLETFGRIDILVNNLAVQFVQNHFVDISDEQWHITFDTN 165 Query: 122 LNGAFYVTQAAAQQMKLQGTGGAIVATSSISALVGGGMQTHYTPTKAGVHSLMQSCAVAL 181 ++ FY+T+AA M G +I+ T+SI+A +G YT TK + S ++ A + Sbjct: 166 IHPFFYMTKAALPHMH---AGSSIINTTSINAYIGRKDLIDYTTTKGAIVSFTRALANNI 222 Query: 182 GPYGIRCNSVMPGTIATDLNAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFLASDRA 241 GIR N+V PG I T L + K F +P+ R G+P ++A LAS Sbjct: 223 VDQGIRVNAVAPGPIWTPLIPASFTPDMVKT-FGSNVPMKRAGQPYELAPVYVLLASSDG 281 Query: 242 RYVTGAALLVDGGLFV 257 Y+TG + ++GG FV Sbjct: 282 SYITGQTIHINGGGFV 297 Lambda K H 0.319 0.134 0.386 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: 167 Number of extensions: 10 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: 260 Length of database: 299 Length adjustment: 26 Effective length of query: 234 Effective length of database: 273 Effective search space: 63882 Effective search space used: 63882 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: 47 (22.7 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