Align Probable galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (uncharacterized)
to candidate AZOBR_RS16155 AZOBR_RS16155 altronate hydrolase
Query= curated2:P42240 (510 letters) >FitnessBrowser__azobra:AZOBR_RS16155 Length = 495 Score = 244 bits (622), Expect = 7e-69 Identities = 170/489 (34%), Positives = 241/489 (49%), Gaps = 30/489 (6%) Query: 13 YIKVHEIDNTAIIVNDGGLPKGTVFS-CGLVLEEDVPQGHKVALTDLNQGDEIVRYGEVI 71 Y+K+H D A+ + L +GT G+VL ++VPQGHK A+T GD +++YG VI Sbjct: 4 YLKIHSSDTVAVALEP--LAQGTAIDGLGIVLLDEVPQGHKFAVTPHQPGDRVIKYGSVI 61 Query: 72 GFADETIKRGSWIREALVRMP---------APPALDDLPLANRVPQPRPPLEGYTFEGYR 122 G A E I G I + A PA D P P T + + Sbjct: 62 GLAKEAIPVGRHIHTHNIGTALGGLQNYAYAGPANDAAPAKREAP---------TIQAFV 112 Query: 123 NADGSAGTKNILGITTSVQCVVGVLDYAVKRIKEELLPKYPNVDDVVPLHHQYGCGVAIN 182 A+G G +N L I V CV G+ A KR E + P V+ L H YGC Sbjct: 113 RANGEVGVRNDLWIIPLVGCVNGLAKNAAKRF--EKMGLLPEGSRVMVLEHPYGCSQLGG 170 Query: 183 APDAVIPIRTIQNLAKHPNFGGEVMVIGLGCE---KLLPERIASENDDDILSLQDHRGFA 239 D I +++ A HPN GG V+V+GLGCE + L + D L + + Sbjct: 171 DLDNTRNI--LRDFAIHPNAGG-VLVMGLGCENNTRALFTQGFEHPDPRRLRYLTTQEVS 227 Query: 240 AMIQSILEMAEERLIRLNSRTRVSCPVSDLVIGLQCGGSDAFSGVTANPAVGYAADLLVR 299 +++ LE E + R L IGL+CGGSD FSG+TANP +G +D L Sbjct: 228 DELEASLEAMTELAAVMREDKREPVGADRLRIGLKCGGSDGFSGITANPLLGALSDWLCG 287 Query: 300 AGATVLFSEVTEVRDAIHLLTPRAVSEEVGQSLIKEMKWYDSYLRRGDADRSANPSPGNK 359 G + +EV E+ A HLL RA S EV ++ + + Y + NPSPGNK Sbjct: 288 IGGATVLTEVPEMFGAEHLLMERAESREVFDGVVTLINDFKQYFIDHNQPIYENPSPGNK 347 Query: 360 KGGLSNVVEKALGSVAKSGTSPISGVLGPGERAKQKGLLFAATPASDFVCGTLQLAAGMN 419 GG+S + EK+LG K+G SP+ V+ ER ++ GL P +D V T AAG + Sbjct: 348 AGGISTLEEKSLGCTQKAGLSPVRDVIRYAERIRKPGLTLLEAPGNDGVAVTALAAAGCH 407 Query: 420 LQVFTTGRGTPYGLAAAPVLKVSTRHSLSEHWADLIDINAGRIATGEASIEDVGWEIFRT 479 + +FTTGRGTP G P +K++T +++E ID NAG IA A+++ + + Sbjct: 408 IVLFTTGRGTPLG-GVVPTMKIATNTAMAEKKRHWIDFNAGPIAEATATVDSLLPSFIDS 466 Query: 480 ILDVASGRK 488 IL VA+G++ Sbjct: 467 ILAVANGKE 475 Lambda K H 0.318 0.136 0.406 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: 673 Number of extensions: 35 Number of successful extensions: 5 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: 510 Length of database: 495 Length adjustment: 34 Effective length of query: 476 Effective length of database: 461 Effective search space: 219436 Effective search space used: 219436 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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