Align L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401) (characterized)
to candidate RR42_RS05150 RR42_RS05150 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase
Query= metacyc::MONOMER-16233 (285 letters) >FitnessBrowser__Cup4G11:RR42_RS05150 Length = 312 Score = 181 bits (458), Expect = 2e-50 Identities = 106/252 (42%), Positives = 145/252 (57%), Gaps = 12/252 (4%) Query: 31 PELTIEALAAAKGADVASLPLVEGEPRYGVPVKGIGKIVAIGLNYEDHAIESNLPIP--- 87 P L A AA+ A L V+ Y VP + G+I + N+ DHA E + Sbjct: 58 PLLADMAGRAAQLATSGKLAAVDAAATYAVPYQP-GRIFGVASNFYDHADEMGTKLAARS 116 Query: 88 -TEPMMFMKALSSLNGPNDEVVLPKNSTHGDWEVELGVVIGETCRFVSEDEALSKVAGYV 146 ++P FMKA +S+ V++P + DWEVELGVVIG+ CR V ++ALS +AGY Sbjct: 117 ESQPYAFMKAETSVIPTGATVLMPPETAKLDWEVELGVVIGQRCRHVPVEDALSVIAGYT 176 Query: 147 LVNDVSERFNQKQRGT----QWSKGKGHDTFCPVGPWLVTPDEVGDPQDLDMHLNVNGTR 202 + ND+S R ++ W +GK DTF P+GPW+V + DPQ+L M L VNG Sbjct: 177 VFNDISARDLNRRTDYPFTHDWFRGKSFDTFGPMGPWVVPAGCIADPQNLRMSLTVNGET 236 Query: 203 MQTGNTKTMIFNVAQLISYVSEYITLYPGDLMITGTPPGVGEGKKPQAIYLKAGDVMELG 262 MQ GNT MIF+VA+ I+Y+S +TL PGDL+ TGTP GVG G+ ++LK GD M Sbjct: 237 MQDGNTSQMIFSVAEQIAYLSRILTLQPGDLIATGTPDGVGMGR---GVFLKPGDNMVAW 293 Query: 263 IEKLGTQRQQVS 274 IE +G+ V+ Sbjct: 294 IEGIGSIENAVA 305 Lambda K H 0.316 0.137 0.411 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: 273 Number of extensions: 14 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: 285 Length of database: 312 Length adjustment: 27 Effective length of query: 258 Effective length of database: 285 Effective search space: 73530 Effective search space used: 73530 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: 42 (22.0 bits) S2: 48 (23.1 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