Align 2-keto-3-deoxy-L-rhamnonate aldolase (EC 4.1.2.53) (characterized)
to candidate 8501164 DvMF_1898 HpcH/HpaI aldolase (RefSeq)
Query= BRENDA::P76469 (267 letters) >FitnessBrowser__Miya:8501164 Length = 259 Score = 124 bits (310), Expect = 3e-33 Identities = 80/245 (32%), Positives = 118/245 (48%), Gaps = 9/245 (3%) Query: 4 LLSNPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQA 63 + + +E++R+GE IG W+ + +AEI SGYDW+ +D EHA T L +A Sbjct: 2 ITARDIREKMRRGEATIGTWMQIPSTDVAEILGRSGYDWVAVDLEHAAFTRSQLPDAFRA 61 Query: 64 VAPYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYP----PYGE 119 + + P R E + IK LD GA+ L+ PM++T EQ + YP P G Sbjct: 62 IELGGAAPFARVAEATLTDIKASLDSGARGLIFPMIETREQLDAAIGWALYPRTDGPSGV 121 Query: 120 RGVGASVARAARWGR-IENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPA 178 RGVG RA +GR Y+ + + Q+E A+DNLD IL +D + +GP Sbjct: 122 RGVG--YCRANLFGREFTPYVNETARDTLFVAQIEHIRAVDNLDAILSHPRLDAIMVGPY 179 Query: 179 DLSASLGYPDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQ--QCLAWGANFVAV 236 DLS S+G HP+ ++ RA G V PD A + + G F+A Sbjct: 180 DLSGSMGLTAQFDHPDFLAALDRIAAAARAHDVPMGLHIVQPDTADLARRIGEGYRFIAW 239 Query: 237 GVDTM 241 +D + Sbjct: 240 CIDAV 244 Lambda K H 0.318 0.134 0.393 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: 154 Number of extensions: 7 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: 267 Length of database: 259 Length adjustment: 25 Effective length of query: 242 Effective length of database: 234 Effective search space: 56628 Effective search space used: 56628 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