Align Probable galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (uncharacterized)
to candidate PP_2834 PP_2834 Putative D-galactarate dehydratase/Altronate dehydratase
Query= curated2:P42240 (510 letters) >FitnessBrowser__Putida:PP_2834 Length = 513 Score = 314 bits (804), Expect = 5e-90 Identities = 190/494 (38%), Positives = 273/494 (55%), Gaps = 16/494 (3%) Query: 5 LRKNQAPLYIKVHEIDNTAIIVNDGGLPKGTVFSCGLVLEEDVPQGHKVALTDLNQGDEI 64 + K+ P I+++ +DN +I LP + + + + + +P GHK+A + QG + Sbjct: 4 IAKSGDPAVIRLNPLDNV-VIARQALLPGVRLDAEAITVRQPIPSGHKLATEPVAQGQPL 62 Query: 65 VRYGEVIGFADETIKRGSWIREALVRMPAPPALDDLPLANRVPQPRPPLEGYTFEGYRNA 124 RYG++IGFA + I G + V+M A D A V P F+G A Sbjct: 63 RRYGQIIGFASQAIDAGDHVHVHNVQM-GDFARD---YAFGVDTRSLPGSAAQFQGIVRA 118 Query: 125 DGSAGTKNILGITTSVQCVV----GVLDYAVKRIKEELLPKYPNVDDVVPLHHQYGCGVA 180 DG T+N +GI TSV C V D+ + I E+L YPNVD VV L H GC V Sbjct: 119 DGRVATRNYIGILTSVNCSATVARAVADHFRRDIHPEVLADYPNVDGVVALSHSAGCAVD 178 Query: 181 INAPDAVIPIRTIQNLAKHPNFGGEVMVIGLGCEK------LLPERIASENDDDILSLQD 234 + + RT+ A HPNF V++IGLGCE L + + + ++Q Sbjct: 179 PSGEALGLLRRTLAGYAVHPNFAA-VLIIGLGCETNQIETLLETQGLQASAQLRAFTIQG 237 Query: 235 HRGFAAMIQSILEMAEERLIRLNSRTRVSCPVSDLVIGLQCGGSDAFSGVTANPAVGYAA 294 G + I + + + L N R LV+GLQCGGSD +SG+TANPA+G A Sbjct: 238 IGGTSKTIAAGIAQVKALLAEANQVRRQPVSARHLVVGLQCGGSDGYSGITANPALGNAV 297 Query: 295 DLLVRAGATVLFSEVTEVRDAIHLLTPRAVSEEVGQSLIKEMKWYDSYLRRGDADRSANP 354 D LV AG T + SE E+ A HLLT RAVS EVG+ L+ ++W++ Y +R +A+ + NP Sbjct: 298 DRLVAAGGTAILSETPEIYGAEHLLTRRAVSREVGEKLVARIRWWEDYCQRMNAELNNNP 357 Query: 355 SPGNKKGGLSNVVEKALGSVAKSGTSPISGVLGPGERAKQKGLLFAATPASDFVCGTLQL 414 S GNK GGL+ ++EK+LG+VAK+G+S + V + + +GL+F TP D V T Q+ Sbjct: 358 SAGNKAGGLTTILEKSLGAVAKAGSSNLVDVYQYAQAVRAQGLVFMDTPGYDPVSATGQV 417 Query: 415 AAGMNLQVFTTGRGTPYGLAAAPVLKVSTRHSLSEHWADLIDINAGRIATGEASIEDVGW 474 A G NL FTTGRG+ YG A AP +K++T + + EH + +D+N G IA G SIE+ G Sbjct: 418 AGGANLIAFTTGRGSAYGCAPAPSIKLATNNRVFEHQQEDMDVNCGGIADGSTSIEERGA 477 Query: 475 EIFRTILDVASGRK 488 IF +L +ASG + Sbjct: 478 FIFEQMLRIASGER 491 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: 664 Number of extensions: 40 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: 513 Length adjustment: 35 Effective length of query: 475 Effective length of database: 478 Effective search space: 227050 Effective search space used: 227050 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