Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate SMc00880 SMc00880 oxidoreductase
Query= reanno::Burk376:H281DRAFT_00644 (263 letters) >FitnessBrowser__Smeli:SMc00880 Length = 256 Score = 124 bits (310), Expect = 3e-33 Identities = 90/264 (34%), Positives = 131/264 (49%), Gaps = 31/264 (11%) Query: 11 PGLR---VFVSAGAAGIGLAIAEAFIEAQAEVYICDVNQAA-------IDEATSRFPKLH 60 P LR V V+ G +GIG A+ EAF A V D+ + + T + P H Sbjct: 9 PDLRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAP--H 66 Query: 61 AGIADVSKQAQVDQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNS 120 AD+ V D+A KLG + VLVNNA A+E + W+ ++S NL Sbjct: 67 FIQADLRNVEAVRAAADEAVAKLGSVRVLVNNAA-RDDRQALEAVTEESWDESLSVNLRH 125 Query: 121 QFYFLRKAVPVLKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPS 180 F+ + P ++ SI+ SS+A L P Y++ K I+GL KSLA +LGP Sbjct: 126 LFFMCQAVAPHMQRQGG-GSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPD 184 Query: 181 NVRVNAILPGVVEGERMDRVISARADALGIPFNAMREEYLKKIS----LRRMVTVDDIAA 236 N+RVNAILPG++ ER R+ + EE + ++ L+RM+ DD+ Sbjct: 185 NIRVNAILPGMIVTERQRRL-------------WLTEESIARMQERQCLKRMLVADDLVG 231 Query: 237 MALFLASPAGSNVTGQAISVDGNV 260 LFLAS + + +T QA+ +DG V Sbjct: 232 PCLFLASDSSAAMTAQAMIIDGGV 255 Lambda K H 0.318 0.134 0.375 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: 121 Number of extensions: 8 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: 263 Length of database: 256 Length adjustment: 24 Effective length of query: 239 Effective length of database: 232 Effective search space: 55448 Effective search space used: 55448 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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