Align Mitochondrial enolase superfamily member 1; Antisense RNA to thymidylate synthase; rTS; L-fuconate dehydratase; EC 4.2.1.68 (characterized)
to candidate PP_2831 PP_2831 L-fuconate dehydratase
Query= SwissProt::Q7L5Y1 (443 letters) >FitnessBrowser__Putida:PP_2831 Length = 411 Score = 525 bits (1351), Expect = e-153 Identities = 248/408 (60%), Positives = 316/408 (77%), Gaps = 4/408 (0%) Query: 28 MHTDPDYSAAYVVIETDAEDGIKGCGITFTLGKGTEVVVCAVNALAHHVLNKDLKDIVGD 87 M++ PDYSAAYVV+ TDA ++G G+TFT+G+G E+ AV +LA ++ L++I D Sbjct: 1 MNSAPDYSAAYVVLHTDAA-ALEGHGLTFTIGRGNEICAAAVQSLAPLIVGLTLEEISAD 59 Query: 88 FRGFYRQLT-SDGQLRWIGPEKGVVHLATAAVLNAVWDLWAKQEGKPVWKLLVDMDPRML 146 F+ + T SD QLRW+GPEKGV+HLATAA++NAVWDLWAK EGKPVWKLL DM P L Sbjct: 60 MGAFWHRFTVSDSQLRWLGPEKGVIHLATAAIINAVWDLWAKHEGKPVWKLLADMTPEQL 119 Query: 147 VSCIDFRYITDVLTEEDALEILQKGQIGKKEREKQMLAQGYPAYTTSCAWLGYSDDTLKQ 206 V C+DF Y+TDVLT E+A+ +L++ GK ERE ML +GYP YTT+ WLGYS++ +++ Sbjct: 120 VRCLDFSYVTDVLTPEEAIALLRRQAPGKAEREAHMLREGYPGYTTAPGWLGYSEEKMRK 179 Query: 207 LCAQALKDGWTRFKVKVGADLQDDMRRCQIIRDMIGPEKTLMMDANQRWDVPEAVEWMSK 266 L +A+ DGWT K K+GADL++D+RR I+RD IG E+TLMMDANQ W V E+V M + Sbjct: 180 LAREAVADGWTHIKQKIGADLEEDIRRASILRDEIGWERTLMMDANQVWGVEESVANMRR 239 Query: 267 LAKFKPLWIEEPTSPDDILGHATISKALVPLGIGIATGEQCHNRVIFKQLLQAKALQFLQ 326 LA F+PLWIEEPTSPDDILGHATI + + P IG+ATGE CHNRV+FKQ+ QA AL F Q Sbjct: 240 LAAFEPLWIEEPTSPDDILGHATIRQRIAP--IGVATGEHCHNRVMFKQMFQAGALDFCQ 297 Query: 327 IDSCRLGSVNENLSVLLMAKKFEIPVCPHAGGVGLCELVQHLIIFDYISVSASLENRVCE 386 +D+ RLG +NE L VLLMA K+++PVCPH GGVGLCE VQ++ +FDYI+VSASL NRV E Sbjct: 298 LDAARLGGLNEVLIVLLMAAKYDVPVCPHGGGVGLCEYVQNIALFDYIAVSASLHNRVLE 357 Query: 387 YVDHLHEHFKYPVMIQRASYMPPKDPGYSTEMKEESVKKHQYPDGEVW 434 YVDHLHEHF PV+I R YMPP+ PGYS EM E+++++QYP+G VW Sbjct: 358 YVDHLHEHFIDPVVIHRGRYMPPQRPGYSIEMHAETLERYQYPNGAVW 405 Lambda K H 0.321 0.137 0.425 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: 578 Number of extensions: 16 Number of successful extensions: 4 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: 443 Length of database: 411 Length adjustment: 32 Effective length of query: 411 Effective length of database: 379 Effective search space: 155769 Effective search space used: 155769 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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