Align D-mannonate dehydratase CC2812; ManD; EC 4.2.1.8 (characterized)
to candidate PfGW456L13_2128 Galactonate dehydratase (EC 4.2.1.6)
Query= SwissProt::Q9A4L8 (403 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2128 Length = 382 Score = 192 bits (487), Expect = 2e-53 Identities = 133/414 (32%), Positives = 208/414 (50%), Gaps = 46/414 (11%) Query: 3 KIIAAKTIVTCPGRNFVTLKIMTDEGVYGLGDATLNGRELAVEAYLTQHVIPCLIGRDAH 62 KI T + P F LK+ TDEGV G G+ + GR V A + + + LIG+D Sbjct: 2 KITKLTTFIVPPRWCF--LKVETDEGVTGWGEPVVEGRAHTVAAAV-EELSDYLIGKDPR 58 Query: 63 QIEDIWQYLYRGCYWRRGPVTMAAIAAVDTALWDIKGKIAGLPVYQLLGGACRVGVMVYG 122 IEDIW LYRG ++R G + M+A+A +D ALWDIKGK G+ V LLGG R + VY Sbjct: 59 NIEDIWTVLYRGGFYRGGAIHMSALAGIDQALWDIKGKALGVSVSDLLGGQVRDKIRVYS 118 Query: 123 HANGETIDETLDNAAVYAQQGYKAIRLQTGVPGMSGTYGVSKDKFFYEPADSDLPKETIW 182 G+ +T A ++G+ A++ M+GT ++ F + D Sbjct: 119 WIGGDRPADTARAAKEAVERGFTAVK-------MNGT----EELQFLDTFDK-------- 159 Query: 183 STERYLRSTPALFEAARERLGDDLHLLHDVHHRLTPIEAARLGKDLEPYRLFWMEDATPA 242 + A A R+ +G ++ + D H R+ A L K+L+PY+L ++E+ + Sbjct: 160 -----VDQALANVAAVRDAVGPNVGIGVDFHGRVHKPMAKVLMKELDPYKLMFIEEPVLS 214 Query: 243 ENQASFRLIRQHTTTPLAVGEIFNSIWDCKQLIEEQLIDYIRATVVHAGGITHLKKLASF 302 EN + + + T+TP+A+GE S WD K+++ E +D I+ HAGGIT +K+A+ Sbjct: 215 ENYEALKELAPLTSTPIALGERLFSRWDFKRVLSEGYVDIIQPDASHAGGITETRKIANM 274 Query: 303 ADLHHVRTGCHGATDLSPVCMGAALHFDLSIPNFGVQEYMR--HTPETDAVF-----PHA 355 A+ + V H L P+ + A L D + N +QE H E++ + P Sbjct: 275 AEAYDVALALH--CPLGPIALAACLQLDAACYNAFIQEQSLGIHYNESNDLLDYVKDPRV 332 Query: 356 YTFKDGMLHPGDAPGLGVDIDEDLAAKYPYQRAYL------PIARRLDGSMHDW 403 + + G + + PGLG++I+E+ Y +RA + PI R DGS +W Sbjct: 333 FDYDKGFVKIPNGPGLGIEINEE----YVIERAAIGHRWRNPIWRHADGSFAEW 382 Lambda K H 0.322 0.139 0.437 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: 383 Number of extensions: 20 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