Align L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401) (characterized)
to candidate BPHYT_RS28880 BPHYT_RS28880 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
Query= metacyc::MONOMER-16233 (285 letters) >FitnessBrowser__BFirm:BPHYT_RS28880 Length = 252 Score = 130 bits (326), Expect = 4e-35 Identities = 76/215 (35%), Positives = 116/215 (53%), Gaps = 9/215 (4%) Query: 53 EGEPRYGVPVKGIGKIVAIGLNYEDHAIESNLPIPTEPMMFMKALSSLNGPNDEVVLPKN 112 E E + P++ +G I A+GLNY +HA E EP++F+K ++ G P + Sbjct: 32 EDEVVWLAPIE-VGTIFALGLNYAEHAKELQFNKQEEPLVFLKGPGTVIGHRGVTRRPAD 90 Query: 113 STHGDWEVELGVVIGETCRFVSEDEALSKVAGYVLVNDVSERFNQKQRGTQWSKGKGHDT 172 T +E EL VVIG+T + V D A+ VAGY++ ND + R + + K D Sbjct: 91 VTFMHYECELAVVIGQTAKNVKRDNAMQHVAGYMIANDYAIRDYLENYYRPNLRVKNRDG 150 Query: 173 FCPVGPWLVTPDEVGDPQDLDMHLNVNGTRMQTGNTKTMIFNVAQLISYVSEYITLYPGD 232 +GPW V +V D L++ VNGTR Q GNT+ ++ + LI Y+S ++TL PGD Sbjct: 151 GTVLGPWFVDAADVEDVTQLELRTFVNGTRQQHGNTRDLVTGIPALIEYLSSFMTLAPGD 210 Query: 233 LMITGTPPGVGEGKKPQAIYLKAGDVMELGIEKLG 267 +++TGTP G+ + + AGD + I+ LG Sbjct: 211 VILTGTPEGI--------VNVNAGDEVVCEIDGLG 237 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: 214 Number of extensions: 10 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: 252 Length adjustment: 25 Effective length of query: 260 Effective length of database: 227 Effective search space: 59020 Effective search space used: 59020 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: 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