Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate AO353_21770 AO353_21770 3-hydroxybutyrate dehydrogenase
Query= reanno::BFirm:BPHYT_RS04775 (263 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21770 Length = 257 Score = 119 bits (298), Expect = 6e-32 Identities = 83/250 (33%), Positives = 131/250 (52%), Gaps = 6/250 (2%) Query: 12 GLRVLISGAAAGIGAAIAQAFLDVGANVYICDVDPAA--IDRARTAHPQLHAGVADVSDC 69 G L++G+ +GIG IA + GAN+ + A+ I + + ++ ADVSD Sbjct: 6 GKTALVTGSTSGIGLGIALSLAKAGANLILNGFGDASTVIAQVQQFGGKVGHHPADVSDP 65 Query: 70 AQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRKAV 129 AQ+ +I A + GG+D+L+NNAGI AVED W+ I NL+S F+ R ++ Sbjct: 66 AQIAEMIAYAEREFGGVDILVNNAGIQH-VSAVEDFPVERWDSIIAINLSSVFHSTRLSL 124 Query: 130 PLLKETSANPGIIAMASVAGRLGYAFRTPYAASKWAIVGMVKSLAIELGPNNVRVNAILP 189 P ++ I+ +ASV G++G + Y A+K ++G+ K + +E +NV NAI P Sbjct: 125 PGMRAKGWGR-IVNIASVHGQVGSVGKAAYVAAKHGVIGLTKVVGLETATSNVTCNAICP 183 Query: 190 GVVEGERMDRVISARAESLGIGFDQMKGEYL-QKISLRRMVTVHDVAAMALFLASPAGQN 248 G V + + I RA + GI Q + + L +K VT + + LFL S AG Sbjct: 184 GWVLTPLVQKQIDDRA-AAGIDPQQAQHDLLAEKQPSLEFVTPSQLGELVLFLCSEAGSQ 242 Query: 249 ISGQAISVDG 258 + G A ++DG Sbjct: 243 VRGAAWNIDG 252 Lambda K H 0.320 0.136 0.391 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: 157 Number of extensions: 8 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: 263 Length of database: 257 Length adjustment: 24 Effective length of query: 239 Effective length of database: 233 Effective search space: 55687 Effective search space used: 55687 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 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