Align Probable galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (uncharacterized)
to candidate SMc02776 SMc02776 altronate hydrolase
Query= curated2:P42240 (510 letters) >FitnessBrowser__Smeli:SMc02776 Length = 501 Score = 303 bits (777), Expect = 7e-87 Identities = 180/486 (37%), Positives = 263/486 (54%), Gaps = 16/486 (3%) Query: 10 APLYIKVHEIDNTAIIVNDGGLPKGTVFSCGLVLEEDVPQGHKVALTDLNQGDEIVRYGE 69 AP I + DN ++V + G + G+ + GHK A+ ++ G+ +V+YG+ Sbjct: 3 APSSILLSPDDN--VVVATAAIAPGDRLAGGVSAVARIEPGHKAAIRRIDVGEPVVKYGQ 60 Query: 70 VIGFADETIKRGSWIREALVRMPAPPALDDLPLANRVPQPRPPL----EGYTFEGYRNAD 125 IG A I G + + A D LA P + TF GYR AD Sbjct: 61 AIGRATSPIAPGEHVHSHNL------AFDQGRLAVGAAVPPEAASEADKARTFLGYRRAD 114 Query: 126 GSAGTKNILGITTSVQCVVGVLDYAVKRIKEELLPKYPNVDDVVPLHHQYGCGVAINAPD 185 G A T+N +GI SV C V +LPKY +D VP+ H GCG++ Sbjct: 115 GRAATRNYIGIVASVNCSTTVCRAIADEANRRILPKYEGIDGFVPIVHDQGCGMSSTGDG 174 Query: 186 AVIPIRTIQNLAKHPNFGGEVMVIGLGCEK---LLPERIASENDDDILSLQDHRGFAAMI 242 RT+ A+H NFGG V+++GLGCE L + + + ++Q+ G + Sbjct: 175 MKNLHRTLAGYARHANFGG-VLMVGLGCEVNQLTLYGQSGAGAEKRHFNIQEAGGSRRSV 233 Query: 243 QSILEMAEERLIRLNSRTRVSCPVSDLVIGLQCGGSDAFSGVTANPAVGYAADLLVRAGA 302 + L + +E + + RV PVS++++GLQCGGSD SG+TANPA+G A D+L AG Sbjct: 234 ERALGILDEIAKEVAAARRVPIPVSEIIVGLQCGGSDGLSGITANPALGAAVDILAAAGG 293 Query: 303 TVLFSEVTEVRDAIHLLTPRAVSEEVGQSLIKEMKWYDSYLRRGDADRSANPSPGNKKGG 362 T + SE +E+ A HLL RAV+E V L + W++ Y+ A NPSPGNK+GG Sbjct: 294 TAILSETSEIYGAEHLLRSRAVNETVAVKLDGLIAWWEDYVAMHGASLDNNPSPGNKRGG 353 Query: 363 LSNVVEKALGSVAKSGTSPISGVLGPGERAKQKGLLFAATPASDFVCGTLQLAAGMNLQV 422 L+ ++EK+LG+VAK G SP++ V ER + GL+F TP D V T Q+A G N+ Sbjct: 354 LTTILEKSLGAVAKGGRSPLTAVYNYAERVTEPGLVFMDTPGYDPVSATGQVAGGANVIA 413 Query: 423 FTTGRGTPYGLAAAPVLKVSTRHSLSEHWADLIDINAGRIATGEASIEDVGWEIFRTILD 482 FTTGRG+ +G AP +K+++ +L + +DI+ G IA+GE +I D+G IF I++ Sbjct: 414 FTTGRGSCFGCRPAPSIKLTSNTALYRAMEEDMDIDCGVIASGETTIADLGRGIFELIIE 473 Query: 483 VASGRK 488 ASGRK Sbjct: 474 TASGRK 479 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: 653 Number of extensions: 33 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: 501 Length adjustment: 34 Effective length of query: 476 Effective length of database: 467 Effective search space: 222292 Effective search space used: 222292 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