Align L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate BPHYT_RS20755 BPHYT_RS20755 fuconate dehydratase
Query= BRENDA::Q8ZL58 (398 letters) >FitnessBrowser__BFirm:BPHYT_RS20755 Length = 432 Score = 110 bits (276), Expect = 6e-29 Identities = 105/384 (27%), Positives = 165/384 (42%), Gaps = 68/384 (17%) Query: 56 PLTEVAIIIAEIRSRDGFEGVGFSYSKRAGGQGIYAHAKEIADNLLGEDPNDIDKIY--- 112 P A + E S D G G +++ G + A + +A ++G+ DI Sbjct: 30 PDYSAAYVTLETDSPDALTGHGLTFTIGRGNEICVAAVEALAPLIVGKRLEDIAANMGAF 89 Query: 113 -------TKLLWAGASVGRSGMAVQAISPIDIALWDMKAKRAGLPLAKLLG--AHRDSVQ 163 ++L W G G +A A+ A WD+ AK G P+ KLL + + V+ Sbjct: 90 WRALTSDSQLRWIGPDKGAIHLATAAVVN---AAWDLWAKAEGKPVWKLLVDMSPEELVR 146 Query: 164 C----------------------------------------YNTSGGFLHTPLDQVLKNV 183 C Y TS G+L D++ + Sbjct: 147 CLDFRYVTDAITPQEAIAMLHRHAKTRGEREKEMLAQGYPAYTTSAGWLGYDDDKIRRLA 206 Query: 184 VISRENGIGGIKLKVGQPNCAEDIRRLTAVREALGDEFPLMVDANQQWDRETAIRMGRKM 243 G K KVG N ED+RR +RE +G++ LM+DANQ WD + A+ R++ Sbjct: 207 REGVAQGWTHFKQKVGG-NLDEDMRRARILREEIGEDRKLMMDANQVWDVDEAVANMRRL 265 Query: 244 EQFNLIWIEEPLDAYDIEGHAQLAAAL-DTPIATGEMLTSFREHEQLILGNASDFVQPDA 302 QF+ WIEEP DI GHA + L +ATGE + +QL+ A DF Q D+ Sbjct: 266 AQFDPWWIEEPTSPDDILGHAAIRQRLRQIGVATGEHCHNRVMFKQLLQAQAIDFCQVDS 325 Query: 303 PRVGGISPFLKIMDLAAKHGRKLAPH--------FAMEVHL--HLSAAYPLE-PWLEHFE 351 R+GG++ + ++ +AAK G + PH + + L ++ + LE LE+ + Sbjct: 326 CRLGGLNEVIVVLLMAAKFGVPVCPHAGGVGLCEYVQHISLFDYICVSASLENRVLEYVD 385 Query: 352 WLNPLFNEQLELRDGRMWISDRHG 375 L+ F + + +R+GR R G Sbjct: 386 HLHEHFVDPVVIRNGRYMPPQRSG 409 Lambda K H 0.319 0.136 0.410 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: 420 Number of extensions: 20 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 398 Length of database: 432 Length adjustment: 31 Effective length of query: 367 Effective length of database: 401 Effective search space: 147167 Effective search space used: 147167 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: 50 (23.9 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