Align galactonate dehydratase (EC 4.2.1.6) (characterized)
to candidate CCNA_02903 CCNA_02903 bifunctional D-altronate/D-mannonate dehydratase
Query= BRENDA::G3YE52 (383 letters) >FitnessBrowser__Caulo:CCNA_02903 Length = 403 Score = 177 bits (450), Expect = 4e-49 Identities = 124/395 (31%), Positives = 194/395 (49%), Gaps = 42/395 (10%) Query: 19 VKIVDEDGQCGWGESTLEGHTEAVEGTLNA-LCKRFQGYEADDIEHIWQMAWRLGFYRGG 77 +KI+ ++G G G++TL G AVE L + G +A IE IWQ +R ++R G Sbjct: 21 LKIMTDEGVYGLGDATLNGRELAVEAYLTQHVIPCLIGRDAHQIEDIWQYLYRGCYWRRG 80 Query: 78 PVFMSAISGIDIALWDLKGRRLGVPIYQLLGGKVRNKLSVYAWIGGDRPSDVEAAGKARL 137 PV M+AI+ +D ALWD+KG+ G+P+YQLLGG R + VY G+ + Sbjct: 81 PVTMAAIAAVDTALWDIKGKIAGLPVYQLLGGACRVGVMVYGHANGETIDETLDNAAVYA 140 Query: 138 AQGFKAIK-------MNATEDINW---------LDSPRALDSSVER-LKTVKA------- 173 QG+KAI+ M+ T ++ D P+ S ER L++ A Sbjct: 141 QQGYKAIRLQTGVPGMSGTYGVSKDKFFYEPADSDLPKETIWSTERYLRSTPALFEAARE 200 Query: 174 -LGLDAAL--DFHGRLHKPMAKQLAKALEPHRPLFLEEPLLSEHPEAIKQLSDQVSCPIA 230 LG D L D H RL A +L K LEP+R ++E+ +E+ + + + + P+A Sbjct: 201 RLGDDLHLLHDVHHRLTPIEAARLGKDLEPYRLFWMEDATPAENQASFRLIRQHTTTPLA 260 Query: 231 LGERLYSRWDVKRFLEDASVDILQPDIAHCGGISELRRIASMAETYDVAIAPH--CPLGS 288 +GE S WD K+ +E+ +D ++ + H GGI+ L+++AS A+ + V H L Sbjct: 261 VGEIFNSIWDCKQLIEEQLIDYIRATVVHAGGITHLKKLASFADLHHVRTGCHGATDLSP 320 Query: 289 IALAACMQVDLATPNFVIQEMSLGMHYNTEAGEYDITSYVKDPSVFAVKDGYVDALTAPG 348 + + A + DL+ PNF +QE Y E D P + KDG + APG Sbjct: 321 VCMGAALHFDLSIPNFGVQE------YMRHTPETDAVF----PHAYTFKDGMLHPGDAPG 370 Query: 349 LGIEVNEELVRQLAVNSEPWPPKEFFGPDGGIREW 383 LG++++E+L + P DG + +W Sbjct: 371 LGVDIDEDLAAKYPYQRAYLPIARRL--DGSMHDW 403 Lambda K H 0.320 0.138 0.429 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: 377 Number of extensions: 23 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: 383 Length of database: 403 Length adjustment: 31 Effective length of query: 352 Effective length of database: 372 Effective search space: 130944 Effective search space used: 130944 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