Align D-mannonate dehydratase Caul1835; ManD; EC 4.2.1.8 (characterized)
to candidate 1937093 b4478 galactonate dehydratase (NCBI)
Query= SwissProt::B0T4L2 (403 letters) >FitnessBrowser__Keio:1937093 Length = 382 Score = 175 bits (443), Expect = 2e-48 Identities = 134/414 (32%), Positives = 196/414 (47%), Gaps = 49/414 (11%) Query: 3 KITAARVVVTCPGRNFVTLKIETSDGVYGVGDATLNGRELPV---VSYLTDHVIPCLIGR 59 KIT R+ P R ++ LKIET +GV G G+ + GR V V L D+ LIG+ Sbjct: 5 KITTYRL----PPR-WMFLKIETDEGVVGWGEPVIEGRARTVEAAVHELGDY----LIGQ 55 Query: 60 DAHRIEDIWQYLYKGAYWRRGPVTMAAIAAVDMALWDIKAKIAGLPLYQLLGGACREGIM 119 D RI D+WQ +Y+ ++R GP+ M+AIA +D ALWDIK K+ P++QL+GG R+ I Sbjct: 56 DPSRINDLWQVMYRAGFYRGGPILMSAIAGIDQALWDIKGKVLNAPVWQLMGGLVRDKIK 115 Query: 120 VYGHANGATIEETLENAAVYAAQGYKAIRLQSGVPGLKGVYGVSKDKFFYEPADGDLPTE 179 Y G + ++ G+ +L +G L Sbjct: 116 AYSWVGGDRPADVIDGIKTLREIGFDTFKL-NGCEEL----------------------- 151 Query: 180 SLWSTEKYLRSAPGLFEAARDKLGWDLHLLHDVHHRLTPIEAGRLGKDLEPYRPFWMEDA 239 L + + +A R+ G + D H R++ A L K+LEPYRP ++E+ Sbjct: 152 GLIDNSRAVDAAVNTVAQIREAFGNQIEFGLDFHGRVSAPMAKVLIKELEPYRPLFIEEP 211 Query: 240 VPAENQASFRLIRQHTTTPLAVGEVFNSIWDCKQLIEEQLIDYIRATVVHAGGITHLRKI 299 V AE + + T PLA GE S +D K+++E I ++ + HAGGIT KI Sbjct: 212 VLAEQAEYYPKLAAQTHIPLAAGERMFSRFDFKRVLEAGGISILQPDLSHAGGITECYKI 271 Query: 300 ASFADLHHVRTGCHGATDLSPIAMAAALHFDLSIPNFGIQE------YMRHTEATDTV-F 352 A A+ + V H L PIA+AA LH D N +QE Y + E D V Sbjct: 272 AGMAEAYDVTLAPH--CPLGPIALAACLHIDFVSYNAVLQEQSMGIHYNKGAELLDFVKN 329 Query: 353 PHAYTFNDGMLHPGDAVGLGVDINETEAAKYPYKRA---YLPIARREDGSMHDW 403 ++ G P GLGV+I+E + ++ K A P+ R ED S+ +W Sbjct: 330 KEDFSMVGGFFKPLTKPGLGVEIDEAKVIEFS-KNAPDWRNPLWRHEDNSVAEW 382 Lambda K H 0.321 0.138 0.434 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: 387 Number of extensions: 17 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: 403 Length of database: 382 Length adjustment: 31 Effective length of query: 372 Effective length of database: 351 Effective search space: 130572 Effective search space used: 130572 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 (21.9 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