Align Probable galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (uncharacterized)
to candidate 350014 BT0486 altronate hydrolase (NCBI ptt file)
Query= curated2:P42240 (510 letters) >FitnessBrowser__Btheta:350014 Length = 496 Score = 257 bits (657), Expect = 6e-73 Identities = 159/481 (33%), Positives = 251/481 (52%), Gaps = 18/481 (3%) Query: 13 YIKVHEIDNTAI-IVNDGGLPKG---TVFSCGLVLEEDVPQGHKVALTDLNQGDEIVRYG 68 Y++++ DN A+ IVN LP G +V + L ED+P GHK AL D +G+ +++YG Sbjct: 5 YLRINPADNVAVAIVN---LPAGEHLSVDGIEITLNEDIPAGHKFALKDFAEGENVIKYG 61 Query: 69 EVIGFADETIKRGSWIREALVRMPAPPALDDLPLANRVPQPRPPLEGYTFEGYRNADGSA 128 IG A K+G W+ E ++ L+ +V P + TF+GYR +G Sbjct: 62 YPIGHARMAKKQGDWMNETNIKTNLAGLLEYTYHPTQVTLDIPH-KNLTFKGYRRKNGDV 120 Query: 129 GTKNILGITTSVQCVVGVLDYAVKRIKEELLPKYPNVDDVVPLHHQYGCGVAINAPDAVI 188 G +N + I +V CV G++ + ++ E K VD +V H YGC D Sbjct: 121 GVRNEIWIIPTVGCVNGIIGQLAEGLRRETEGK--GVDAIVAFPHNYGCSQL--GDDHEN 176 Query: 189 PIRTIQNLAKHPNFGGEVMVIGLGCEKLLPE---RIASENDDDILSLQDHRGFAAMIQSI 245 + ++++ HPN G V+++GLGCE P+ + D D + + + Sbjct: 177 TKKILRDMVLHPN-AGAVLIVGLGCENNQPDVFREFLGDYDQDRVKFMVTQKVGDEYEEG 235 Query: 246 LEMAEERLIRLNSRTRVSCPVSDLVIGLQCGGSDAFSGVTANPAVGYAADLLVRAGATVL 305 +++ + + + R P+S+L +GL+CGGSD FSG+TANP +G +D L+ G T + Sbjct: 236 MDILRDLYAKASKDERTEVPLSELRVGLKCGGSDGFSGITANPLLGMFSDFLIAQGGTSV 295 Query: 306 FSEVTEVRDAIHLLTPRAVSEEVGQSLIKEMKWYDSYLRRGDADRSANPSPGNKKGGLSN 365 +EV E+ A +L R ++++ + + + + Y NPSPGNK GG+S Sbjct: 296 LTEVPEMFGAETILMNRCENKDLFEQTVHLINDFKEYFLSHGEPVGENPSPGNKAGGIST 355 Query: 366 VVEKALGSVAKSGTSPISGVLGPGERAKQKGLLFAATPASDFVCGTLQLAAGMNLQVFTT 425 + EKALG K G S +SGV+ GER ++KGL + P +D V T A+G ++ +FTT Sbjct: 356 LEEKALGCTQKCGKSYVSGVMPYGERLQKKGLNLLSAPGNDLVAATTLAASGCHMVLFTT 415 Query: 426 GRGTPYGLAAAPVLKVSTRHSLSEHWADLIDINAGRIATGEASIEDVGWEIFRTILDVAS 485 GRGTP+G P +K+ST +L+++ ID NAG I E +E ++ VAS Sbjct: 416 GRGTPFG-TFVPTMKISTNSTLAKNKPGWIDFNAGVIVENE-PMEKTCERFIEYVIKVAS 473 Query: 486 G 486 G Sbjct: 474 G 474 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: 623 Number of extensions: 41 Number of successful extensions: 6 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: 496 Length adjustment: 34 Effective length of query: 476 Effective length of database: 462 Effective search space: 219912 Effective search space used: 219912 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