Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate 353297 BT3771 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file)
Query= metacyc::MONOMER-20835 (262 letters) >FitnessBrowser__Btheta:353297 Length = 248 Score = 133 bits (334), Expect = 4e-36 Identities = 86/253 (33%), Positives = 128/253 (50%), Gaps = 17/253 (6%) Query: 12 GLRVLISGGAAGIGEVLAAAYLEAGAQVHVCD--VSESALAVFRDKYPGTVATRADVSDA 69 G +++G A GIG+ +A + GA + D + E+A + V + S+A Sbjct: 6 GKTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMGVKAKGYASNA 65 Query: 70 AQIEAVFKVQRE---HLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAH 126 A E KV E G +D+LVNNAGI G + +S+ +W IN+NL + + F H Sbjct: 66 ANFEDTAKVVEEIHKDFGRIDILVNNAGITRD-GLMMRMSEQQWDMVINVNLKSAFNFIH 124 Query: 127 HAVPMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNAL 186 P++ G ++++ASV G G A + YAA+K ++ L KS+A ELG IR NA+ Sbjct: 125 ACTPVMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQELGSRGIRANAI 184 Query: 187 LPGIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAAR 246 PG + + E+R E+ KI L+R T EDVA +A FL S + Sbjct: 185 APGFI-----------LTDMTAALSDEVRAEWAKKIPLRRGGTPEDVANIATFLASDMSS 233 Query: 247 NVTGQAISVDGNV 259 V+GQ I VDG + Sbjct: 234 YVSGQVIQVDGGM 246 Lambda K H 0.318 0.133 0.383 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: 146 Number of extensions: 6 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: 262 Length of database: 248 Length adjustment: 24 Effective length of query: 238 Effective length of database: 224 Effective search space: 53312 Effective search space used: 53312 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