Align Altronate dehydratase; EC 4.2.1.7; D-altronate hydro-lyase (uncharacterized)
to candidate GFF376 Psest_0377 galactarate dehydratase
Query= curated2:O34673 (497 letters) >FitnessBrowser__psRCH2:GFF376 Length = 521 Score = 239 bits (610), Expect = 2e-67 Identities = 168/487 (34%), Positives = 249/487 (51%), Gaps = 20/487 (4%) Query: 5 IKIHKQDNVLLALRD--IQKGERLHAYGVSIEVKDDIKRGHKIALQSIKENDSIVKYGFP 62 I++++ DNV + + D + G + V++E + + HK+AL I E + + +YG Sbjct: 17 IRLNEADNVAVVVNDGGVPVGAQFEGGLVTVEA---VPQSHKVALVDIGEGEPVRRYGQI 73 Query: 63 IGHASQDISIGEHIHVHNTKTNLSDIQLYSYTPRFDENPYSN---ENRTFKGFRRENGDA 119 IG+A + I G V T+ + PR P + TF+GFR +G Sbjct: 74 IGYALEPIRCGSW--VKETQLKMPSAPPLESLPRATAVPDKLAPLDGYTFEGFRNSDGTV 131 Query: 120 GVRNELWIVPTVGCVNGIAEKMLQRFVRETGDIAP-FDNVLVLKHQYGCSQLGDDHENTK 178 G RN L I TV CV G+ E ++R E P D+V+ L H YGC + + Sbjct: 132 GTRNILGISTTVQCVTGVLEHAVKRIRDELLPKYPNVDDVVALTHSYGCGVAINARDAYI 191 Query: 179 QI--LLNAIRHPNAGG-VLVLGLGCENNELAR-MKEALQDVNLKR---VKFLESQSVTDE 231 I + N R+PN GG LV+ LGCE + + M E V+L+ + ES S E Sbjct: 192 PIRTVRNLARNPNLGGEALVISLGCEKLQAEQVMHEGDPSVDLREPWLYRLQESNSGFGE 251 Query: 232 MEAGVALLKEIH-EAAKGDKREDIPLSELKIGLKCGGSDGFSGITANPLLGRFSDYLIAQ 290 M + L E + +RE +P SEL +G++CGGSD FSGITANP LG +D L+ Sbjct: 252 MIEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYAADLLVRA 311 Query: 291 GGSTVLTEVPEMFGAETILMQRAANEEVFHKIVDLINDFKQYFIKHDQPVYENPSPGNKA 350 G + + +E E+ A +L RA EV ++ ++ + +Y + N +PGNK Sbjct: 312 GATVMFSENTEVRDAVYMLTARAETPEVADALIAEMDWYDRYLERGAADRSANTTPGNKK 371 Query: 351 GGISTLEDKSLGCTQKAGISPVTDVLKYGEVLKTKGLTLLSAPGNDLIASSALAAAGCQI 410 GG+S + +KSLG K+G ++ V+ G + KGL + P +D + + AAG + Sbjct: 372 GGLSNIVEKSLGSIVKSGSGAISGVVGPGGRVARKGLIFCATPASDFVCGTLQLAAGMNL 431 Query: 411 VLFTTGRGTPFG-TFVPTVKVATNTELYEAKPHWIDFNAGLLAEDDVHEEYVLREFIHYM 469 +FTTGRGTP+G P VKVAT TEL E P ID +AG +A E + E HY Sbjct: 432 HVFTTGRGTPYGLAMAPVVKVATRTELAERWPDLIDIDAGRIASGRASIEELGWELFHYY 491 Query: 470 IEVASGQ 476 ++VASG+ Sbjct: 492 LDVASGR 498 Lambda K H 0.317 0.137 0.394 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: 570 Number of extensions: 24 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: 497 Length of database: 521 Length adjustment: 34 Effective length of query: 463 Effective length of database: 487 Effective search space: 225481 Effective search space used: 225481 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 (21.6 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