Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate AO353_23170 AO353_23170 short-chain dehydrogenase
Query= metacyc::MONOMER-20835 (262 letters) >FitnessBrowser__pseudo3_N2E3:AO353_23170 Length = 254 Score = 114 bits (285), Expect = 2e-30 Identities = 88/263 (33%), Positives = 129/263 (49%), Gaps = 20/263 (7%) Query: 1 MSVLQRLQPYPGLRVLISGGAAGIGEVLAAAYLEAGAQVHVCD-----VSESALAVFRDK 55 M+ L RL G RVL++GGA G+G A A AGA V + D V +SA + + Sbjct: 1 MTTLNRL--LEGRRVLVTGGARGLGYAFAQAIGRAGAHVVIADILAERVQQSAAELVAEG 58 Query: 56 YPGTVATRADVSDAAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGI-DAISDAEWQATI 114 D++ I+ LGGLD LVNNA I G + +S W + Sbjct: 59 LT-VHGVAVDLAQPDSIDTCVAETTRLLGGLDGLVNNASITNSGGKTCEELSLDTWDQVM 117 Query: 115 NINLTAQYRFAHHAVPMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLAS 174 ++N+ + +P L+ S HG ++++AS G Y A+K AI+ + +SLA Sbjct: 118 HVNVRGTWLMTKACLPALRASGHGAIVNLASDTPLWGAPNLLAYVASKGAIIAMTRSLAR 177 Query: 175 ELGESDIRVNALLPGIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVA 234 ELG +I VNA+ PG+V ++ A A VPEA R Y + +++R EDV+ Sbjct: 178 ELGTDNITVNAIAPGLV-------LVEATAY---VPEARHRL-YNEQRAIQRPQLPEDVS 226 Query: 235 AMALFLCSPAARNVTGQAISVDG 257 LF S AR +TGQ + V+G Sbjct: 227 GAVLFALSDLARFITGQTLPVNG 249 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: 153 Number of extensions: 7 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: 262 Length of database: 254 Length adjustment: 24 Effective length of query: 238 Effective length of database: 230 Effective search space: 54740 Effective search space used: 54740 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