Align Altronate dehydratase; EC 4.2.1.7; D-altronate hydro-lyase (uncharacterized)
to candidate GFF829 PS417_04210 galactarate dehydrogenase
Query= curated2:O34673 (497 letters) >FitnessBrowser__WCS417:GFF829 Length = 517 Score = 253 bits (645), Expect = 1e-71 Identities = 170/488 (34%), Positives = 257/488 (52%), Gaps = 22/488 (4%) Query: 5 IKIHKQDNVLLALRD--IQKGERLHAYGVSIEVKDDIKRGHKIALQSIKENDSIVKYGFP 62 I++H++DNV++ + D + G V++ D I + HK+ L+ I E I++YG Sbjct: 13 IRLHERDNVVIVVNDQGVPAGTEFPDGLVTV---DFIPQSHKVTLEDIPEGGQIIRYGQT 69 Query: 63 IGHASQDISIGEHIHVHN----TKTNLSDIQLYSYTPRFDENPYSNENRTFKGFRRENGD 118 IG+A I G + T L + L + P E E TF+G+R +G Sbjct: 70 IGYALAPIPRGSWVQEDQLRMPTAPPLDSLPLSTEVP---EAQAPLEGFTFEGYRNADGT 126 Query: 119 AGVRNELWIVPTVGCVNGIAEKMLQRFVRETGDIAPF-DNVLVLKHQYGCSQL--GDDHE 175 G RN L I TV CV G+ + ++R E P D+V+ L H YGC D Sbjct: 127 VGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVVALTHSYGCGVAITATDAY 186 Query: 176 NTKQILLNAIRHPNAGG-VLVLGLGCENNELARM---KEALQDVNLKRVKFLESQS--VT 229 + + N R+PN GG LV+ LGCE + ++ ++ D++ + L+ S T Sbjct: 187 IPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMHDNDSSVDLSEPWLYRLQDSSHGFT 246 Query: 230 DEMEAGVALLKEIHEAAKGDKREDIPLSELKIGLKCGGSDGFSGITANPLLGRFSDYLIA 289 + +E +AL + + +RE +P SEL +G++CGGSD FSGITANP LG SD L+ Sbjct: 247 EMIEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYASDLLLR 306 Query: 290 QGGSTVLTEVPEMFGAETILMQRAANEEVFHKIVDLINDFKQYFIKHDQPVYENPSPGNK 349 G + + +EV E+ A +L RA N +V ++V ++ + +Y K + N +PGNK Sbjct: 307 AGATVMFSEVTEVRDAIYLLTSRAENTQVAQELVREMDWYDRYLAKGEADRSANTTPGNK 366 Query: 350 AGGISTLEDKSLGCTQKAGISPVTDVLKYGEVLKTKGLTLLSAPGNDLIASSALAAAGCQ 409 GG+S + +KSLG K+G S + VL GE K KGL + P +D + + AAG Sbjct: 367 KGGLSNIVEKSLGSIVKSGSSAINGVLGPGERFKGKGLIFCATPASDFVCGTLQLAAGMN 426 Query: 410 IVLFTTGRGTPFG-TFVPTVKVATNTELYEAKPHWIDFNAGLLAEDDVHEEYVLREFIHY 468 + +FTTGRGTP+G P VKV+T TEL + P ID +AG +A E + E H+ Sbjct: 427 LHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRATIEELGWELFHF 486 Query: 469 MIEVASGQ 476 ++VASG+ Sbjct: 487 YLDVASGR 494 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: 599 Number of extensions: 25 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: 497 Length of database: 517 Length adjustment: 34 Effective length of query: 463 Effective length of database: 483 Effective search space: 223629 Effective search space used: 223629 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