Align D-mannonate dehydratase Caul1835; ManD; EC 4.2.1.8 (characterized)
to candidate BPHYT_RS10980 BPHYT_RS10980 2-dehydro-3-deoxy-6-phosphogalactonate aldolase
Query= SwissProt::B0T4L2 (403 letters) >FitnessBrowser__BFirm:BPHYT_RS10980 Length = 415 Score = 311 bits (797), Expect = 2e-89 Identities = 176/397 (44%), Positives = 238/397 (59%), Gaps = 23/397 (5%) Query: 4 ITAARVVVTCP-GRNFVTLKIETSD-GVYGVGDATLNGRELPVVSYLTDHVIPCLIGRDA 61 IT +V++T P G N + +K+ET+ G+YG+G +T R + V + +++ P LIGRDA Sbjct: 5 ITDVKVILTAPEGINLIVVKVETNQPGLYGLGCSTFAYRHVAVQCLIEEYLRPLLIGRDA 64 Query: 62 HRIEDIWQYLYKGAYWRRGPVTMAAIAAVDMALWDIKAKIAGLPLYQLLGGACREGIMVY 121 IE++WQ +++ AYWR GP+ AI+ VDMALWDIK K+A +PLYQL GG CREG+ +Y Sbjct: 65 DAIEELWQLMHQNAYWRNGPIENNAISGVDMALWDIKGKLANMPLYQLFGGKCREGVPIY 124 Query: 122 GHANGATIEETLENAAVYAAQGYKAIRLQSGVPGLKGVYGVSKDKFFYEPADGDLPTESL 181 HA+G + E EN Y QG IR QSG G G +G + + ADG Sbjct: 125 RHADGRDLNELCENIQKYREQGITHIRCQSGGYG-GGGFGKAPASAPHGSADG-----VY 178 Query: 182 WSTEKYLRSAPGLFEAARDKLGWDLHLLHDVHHRLTPIEAGRLGKDLEPYRPFWMEDAVP 241 + KY+R LF+ R K+G+D+ L HDVH RL P+EA R +LE Y F++EDA+ Sbjct: 179 LDSRKYMRDTLKLFDGIRSKIGFDVALCHDVHERLKPVEAIRFACELERYELFFLEDAIA 238 Query: 242 AENQASFRLIRQHTTTPLAVGEVFNSIWDCKQLIEEQLIDYIRATVVHAGGITHLRKIAS 301 E R +R TTTPLA GE+FN+ ++ + LI E+LID+IR + GGIT RK+ Sbjct: 239 LEEGEWMRQLRAKTTTPLAQGELFNNPYEWRFLITERLIDFIRVHLSQIGGITAARKLQI 298 Query: 302 FADLHHVRTGCHGATDLSPIAMAAALHFDLSIPNFGIQEYMRHTE--------------A 347 FA+ VRT HG D+SP+A AA +H DL+ NFG+QE+ TE A Sbjct: 299 FAEQFGVRTAWHGPGDMSPLAHAANIHIDLAARNFGVQEW-SGTEPPNFVIQDLKGPRAA 357 Query: 348 TDTVFPHAYTFNDGMLHPGDAVGLGVDINETEAAKYP 384 VFP F G ++ D GLGVDI+E EAAKYP Sbjct: 358 LLDVFPGLPEFRQGYVYANDKPGLGVDIDEAEAAKYP 394 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: 539 Number of extensions: 27 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: 403 Length of database: 415 Length adjustment: 31 Effective length of query: 372 Effective length of database: 384 Effective search space: 142848 Effective search space used: 142848 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