Align Short-chain dehydrogenase (characterized, see rationale)
to candidate SMa0329 SMa0329 short chain alcohol dehydrogenase-related dehydrogenase
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__Smeli:SMa0329 Length = 253 Score = 115 bits (287), Expect = 1e-30 Identities = 91/264 (34%), Positives = 131/264 (49%), Gaps = 28/264 (10%) Query: 1 MDLNLQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQP----- 55 M KV IVTGG SGIG AI+ +L EGA ++ R+E RL+ + Sbjct: 1 MSKRFDGKVAIVTGGGSGIGAAIANRLLEEGASVMMSGRTEK------RLSDVASKMPAD 54 Query: 56 RAALFQLELQDEARCGEAVAETVRRFGRLDGLVNNAGVNDSVGL-----DAGRNEFVASL 110 R+ +F + C VA TV RFGR+D +VN AG+N VG D +E +AS Sbjct: 55 RSGIFVANVSSRPDCDALVAATVERFGRIDTVVNAAGMN-FVGTIQETSDQDWDECIAS- 112 Query: 111 ERNLIHYYVMAHYCVPHLKATRGAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAA 170 +L + M+ VPHLK T+G+I+N+ S ++L G + + Y A+KG +LTR A Sbjct: 113 --DLSGVFYMSRAAVPHLKETKGSIVNIGSVSSLGGGWSHAAYNAAKGGVANLTRSAACD 170 Query: 171 LRDDGVRVNALIPAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVF 230 L GVR N + P +T + E + L+ +IPL + + + A F Sbjct: 171 LGKFGVRANTVAPGLTVTGMVE----AIMDDDALLEKAWDRIPLRR----AGQPASAVAF 222 Query: 231 LLSGRSSHTTGQWVFVDGGYTHLD 254 L S ++ TG + VDGG T D Sbjct: 223 LASDEAAWITGIVLPVDGGQTCTD 246 Lambda K H 0.318 0.134 0.394 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: 9 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: 258 Length of database: 253 Length adjustment: 24 Effective length of query: 234 Effective length of database: 229 Effective search space: 53586 Effective search space used: 53586 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 (21.7 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