Align galactonate dehydratase (EC 4.2.1.6) (characterized)
to candidate CCNA_00566 CCNA_00566 mannonate dehydratase
Query= BRENDA::G3Y8T6 (383 letters) >FitnessBrowser__Caulo:CCNA_00566 Length = 403 Score = 184 bits (466), Expect = 5e-51 Identities = 123/374 (32%), Positives = 186/374 (49%), Gaps = 44/374 (11%) Query: 19 VKVTDSEDKFGWGEATLEGHTQAVEGAL-DEIIGRIVGYEADDIEHVWQTIWRLGFYRGG 77 +K+T + G G+ATL G +V L D ++ ++G +A IE +WQ +R ++RGG Sbjct: 21 LKITTEDGITGVGDATLNGRELSVVSFLQDHMVPSLIGRDAHQIEDIWQFFYRGSYWRGG 80 Query: 78 PVFMSALSGIDIALWDLKGRRLNVPVYQLLGGKVRNKVQVYAWIGGDRPSDVEVAAKARI 137 PV M+AL+ +D+ALWD+KG+ +PVYQLLGG R V VY G+ D A Sbjct: 81 PVAMTALAAVDMALWDIKGKVAGLPVYQLLGGACRTGVTVYGHANGETIEDTIAEAVKYK 140 Query: 138 AQGLKCVKMN---------------------ATEDM---NWLDSPSVLDSC---IERIKQ 170 A G K +++ A D+ N + L+S ER ++ Sbjct: 141 AMGYKAIRLQTGVPGLASTYGVSKDKMFYEPADNDLPTENIWSTAKYLNSVPKLFERARE 200 Query: 171 VKALGLDAGL--DFHGRLHRPMAKQLAKALEPYRPLFIEEPLLVEHPEAIKQLSQHTTIP 228 V LG D L D H RL A +L K LEPYR ++E+ + E+ + + QHTT P Sbjct: 201 V--LGWDVHLLHDVHHRLTPIEAARLGKDLEPYRLFWLEDSVPAENQAGFRLIRQHTTTP 258 Query: 229 IAFGERLYTRWDVKRFLEDASVDVLQPDIAHAGGISETKRIATMAETYDVAIAPH--CPL 286 +A GE WD K+ +E+ +D L+ + HAGGI+ K+IA A+ + V H L Sbjct: 259 LAVGEIFAHVWDAKQLIEEQLIDYLRATVLHAGGITNLKKIAAFADLHHVKTGCHGATDL 318 Query: 287 GPIALAASMQVALSTPNFVIQEMSLGMHYNVEAGDIDLTSYLTNPTVFNIEEGYVPAPTG 346 P+ +AA++ +S NF +QE M + E + P + +G + Sbjct: 319 SPVTMAAALHFDMSITNFGLQEY---MRHTPETDAV-------FPHAYTFSDGMLHPGDK 368 Query: 347 AGLGVEIDEELVRR 360 GLGV+IDE+L + Sbjct: 369 PGLGVDIDEDLAAK 382 Lambda K H 0.320 0.138 0.425 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: 440 Number of extensions: 30 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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