Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate YP_425365.1 Rru_A0273 3-oxoacyl-ACP reductase
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >NCBI__GCF_000013085.1:YP_425365.1 Length = 242 Score = 127 bits (320), Expect = 2e-34 Identities = 86/253 (33%), Positives = 128/253 (50%), Gaps = 15/253 (5%) Query: 2 LLKDKVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEALG 61 + K +V +VTGG+RGIG AI++A G VA NY+G++ A AE E Sbjct: 1 MTKGRVALVTGGTRGIGAAISLALRDAGYRVAANYYGND--------AAAERFTE----E 48 Query: 62 RRVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTVAVN 121 ++ A + +VA Q+ V+ G ++VL +NAGI M PE E + N Sbjct: 49 NKIPAFKFDVAEYAAVQEGVKQITAELGPIEVLVNNAGITRDGTMHRMTPEQWEEVIHTN 108 Query: 122 LNGAFYVTQAAAQQMKLQGTGGAIVATSSISALVGGGMQTHYTPTKAGVHSLMQSCAVAL 181 L+ F + + M+ +G G IV SI+ G Q +Y K+G+H ++ A Sbjct: 109 LSSCFNLARGVIDSMRDRGFG-RIVNIGSINGQAGQYGQVNYAAAKSGIHGFTKALAQEA 167 Query: 182 GPYGIRCNSVMPGTIATDLNAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFLASDRA 241 GI N++ PG + TD+ +K +IP+GRLGR ED+A V FL +D A Sbjct: 168 AAKGITVNAIAPGYVDTDMVRAVPYHVLEKII--AKIPMGRLGRAEDIARGVLFLVADDA 225 Query: 242 RYVTGAALLVDGG 254 Y+TGA L ++GG Sbjct: 226 DYITGATLSINGG 238 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: 154 Number of extensions: 11 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: 242 Length adjustment: 24 Effective length of query: 236 Effective length of database: 218 Effective search space: 51448 Effective search space used: 51448 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: 46 (22.3 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