Align D-galactonate dehydratase; EC 4.2.1.6 (characterized)
to candidate WP_011842465.1 RSPH17029_RS18080 mandelate racemase/muconate lactonizing enzyme family protein
Query= CharProtDB::CH_024133 (382 letters) >NCBI__GCF_000015985.1:WP_011842465.1 Length = 387 Score = 184 bits (468), Expect = 3e-51 Identities = 119/370 (32%), Positives = 191/370 (51%), Gaps = 16/370 (4%) Query: 1 MKITKITTYRLPPRWMFLKIETDEGVVGWGEPVIEGRARTVEAAVHELGDYLIGQDPSRI 60 MKI + R+ +++F++I TD G+VG GE G EAA+ + DYLIG+DP RI Sbjct: 1 MKIVRARPRRVG-QFLFVEITTDSGIVGIGESGAWGHLEASEAALAKYCDYLIGEDPRRI 59 Query: 61 NDLWQVMYRAGFYRGGPILMSAIAGIDQALWDIKGKVLNAPVWQLMGGLVRDKIKAYSWV 120 WQVM+R + G I AI+ +D ALWDIK + P+++L+GG VRD ++ Y+ V Sbjct: 60 ERHWQVMHRFAHFNGAAI-GGAISAVDIALWDIKARSYGVPIYELLGGAVRDSLRVYAHV 118 Query: 121 GGDRPADVI--------DGIKTLREIGFDTFKLNGCEELGLIDNSRAVDAAVNTVAQIRE 172 +V+ DG + F+ F ++ + ++ V + TV + RE Sbjct: 119 YSKTVDEVVSFAAEKARDGYTAIGH--FNPFLDEPEDKPYFLGHAGLVRMGIETVRRTRE 176 Query: 173 AFGNQIEFGLDFHGRVSAPMAKVLIKELEPYRPLFIEEPVLAEQAEYYPKLAAQTHIPLA 232 A G +++ L+ H R++ A + Y P ++E+P+ E + ++A ++ +P+A Sbjct: 177 AVGPEVDLLLEMHRRLTPAEAISFAEAAADYTPGWLEDPIRPENIDAMAEVARRSPVPIA 236 Query: 233 AGERMFSRFDFKRVLEAGGISILQPDLSHAGGITECYKIAGMAEAYDVTLAPHCPLGPIA 292 GER F+ + FK +E +S + + GGIT KIA +AEA DV +APH P+ P+ Sbjct: 237 TGERYFNIYQFKMAIERRALSFARVSVGICGGITAAVKIAAIAEANDVQVAPHNPISPVG 296 Query: 293 LAACLHIDFVSYNAVLQEQSMGIH---YNKGAELLDFVKNKEDFSMVGGFFKPLTKPGLG 349 +AAC + F +QE G + +LL D + GF + GLG Sbjct: 297 VAACAALGFSRSCVAIQEFPTGYDNYVFESTPQLLGRNIVDGDLVVEKGFLQRSEAIGLG 356 Query: 350 VEI-DEAKVI 358 V + D+A+ I Sbjct: 357 VTLKDDAETI 366 Lambda K H 0.321 0.140 0.433 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: 342 Number of extensions: 15 Number of successful extensions: 3 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: 382 Length of database: 387 Length adjustment: 30 Effective length of query: 352 Effective length of database: 357 Effective search space: 125664 Effective search space used: 125664 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 24 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