Align 2,4-diketo-3-deoxy-L-rhamnonate hydrolase (EC 3.7.1.-) (characterized)
to candidate BPHYT_RS28740 BPHYT_RS28740 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
Query= reanno::BFirm:BPHYT_RS34210 (282 letters) >FitnessBrowser__BFirm:BPHYT_RS28740 Length = 296 Score = 350 bits (898), Expect = e-101 Identities = 167/277 (60%), Positives = 213/277 (76%), Gaps = 1/277 (0%) Query: 1 MKLLRYGPKGQEKPGLLDAQGKIRDLSKVVADIDGAALTDEGLAKLRALDPASLPLVEGN 60 M+L+R+G GQE PG++D+ G IRDLS +V+DIDG ++ LAKL LD LPLVE Sbjct: 1 MRLVRFGLPGQEHPGIIDSSGAIRDLSGIVSDIDGTTVSPVALAKLGELDLDRLPLVEAG 60 Query: 61 PRMGPCVGKIGKFICIGLNYADHAAESNLPVPAEPVIFNKWTSAISGPNDDVEIPRGSKK 120 R+G CVG + +CIGLNY+DHAAE++ P+P EPV+FNK T +ISGPND V +P ++K Sbjct: 61 TRLGACVGNVRNLVCIGLNYSDHAAETDTPIPREPVVFNKHTGSISGPNDPVILPADAQK 120 Query: 121 TDWEVELGVVIGKPAKYIDEANALDYVAGYCVINDVSEREWQIEKGGTWDKGKGFDTFGP 180 DWEVELGVVIGKPA IDEA+AL++VAGYC+ NDVSER +Q+E+ G W KGK +F P Sbjct: 121 LDWEVELGVVIGKPAWQIDEADALEHVAGYCLANDVSERAYQLEREGQWTKGKSGFSFAP 180 Query: 181 IGPWVVTRDEVADPQNLSLWLEVDGHRYQNGSTKTMVFGVAKLVSYVSQCMSLQPGDVIS 240 +GPW+VTRDE+ DPQ L LWL+V+G R Q G+T+TM+F +A +V+Y+S+ M L GDVI Sbjct: 181 LGPWLVTRDEIPDPQVLDLWLDVNGTRRQTGNTRTMIFNIAHIVAYLSRFMPLMAGDVII 240 Query: 241 TGTPPGVGMGVKPNPVFLKPGQTIRLGIEGLGEQTQK 277 TGTPPGVG+G KP PVFLK G T+ LG GLGEQ+QK Sbjct: 241 TGTPPGVGLGQKP-PVFLKAGDTMTLGGSGLGEQSQK 276 Lambda K H 0.315 0.138 0.422 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: 354 Number of extensions: 17 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: 282 Length of database: 296 Length adjustment: 26 Effective length of query: 256 Effective length of database: 270 Effective search space: 69120 Effective search space used: 69120 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 (21.9 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