Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate RR42_RS10315 RR42_RS10315 short-chain dehydrogenase
Query= reanno::Burk376:H281DRAFT_00644 (263 letters) >FitnessBrowser__Cup4G11:RR42_RS10315 Length = 253 Score = 190 bits (482), Expect = 3e-53 Identities = 104/249 (41%), Positives = 146/249 (58%), Gaps = 1/249 (0%) Query: 14 RVFVSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDEATSRFPKLHAGIADVSKQAQVD 73 RV V+ GA +G IAE F + A V+ICDV A++ + P + +A+V A V Sbjct: 4 RVIVTGGADSVGRVIAEQFRASGARVHICDVRADALEATLAANPGMTGTVANVGDPAGVA 63 Query: 74 QIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFLRKAVPVLK 133 +++ DA R G + VLVNN GIAGP A+E++ W T+ N+ + F F+++ VP +K Sbjct: 64 RVVQDAERVFGDVSVLVNNVGIAGPRAALEDISDDDWRDTMEVNVGAMFQFMKRVVPSMK 123 Query: 134 ETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVNAILPGVVE 193 II S+ + R P RTPY +K A+ L + A ELGP NVR NAILPG+++ Sbjct: 124 RNRH-GVIINFSTGSTRTRLPMRTPYVVSKAAVESLTLNAARELGPFNVRCNAILPGMID 182 Query: 194 GERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASPAGSNVTGQA 253 ERM R+++ A G + +YLK ISLR V DD+A LFLAS A S +TG+ Sbjct: 183 NERMGRIVAGIAHESGRSAADVEADYLKYISLRCKVQPDDLAQTVLFLASGAASKITGEL 242 Query: 254 ISVDGNVEY 262 I+V GNVE+ Sbjct: 243 IAVSGNVEW 251 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: 169 Number of extensions: 5 Number of successful extensions: 2 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: 253 Length adjustment: 24 Effective length of query: 239 Effective length of database: 229 Effective search space: 54731 Effective search space used: 54731 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