Align Altronate dehydratase; EC 4.2.1.7; D-altronate hydro-lyase (uncharacterized)
to candidate 17201 b3128 (D)-galactarate dehydrogenase (NCBI)
Query= curated2:O34673 (497 letters) >FitnessBrowser__Keio:17201 Length = 523 Score = 247 bits (631), Expect = 6e-70 Identities = 167/492 (33%), Positives = 261/492 (53%), Gaps = 25/492 (5%) Query: 4 FIKIHKQDNVLLALRD--IQKGERLHAYGVSIEVKDDIKRGHKIALQSIKENDSIVKYGF 61 +IK+H DNV + + D ++ G R + +E+ + I +GHK+AL I N I++YG Sbjct: 15 YIKVHDTDNVAIIVNDNGLKAGTR---FPDGLELIEHIPQGHKVALLDIPANGEIIRYGE 71 Query: 62 PIGHASQDISIG----EHIHVHNTKTNLSDIQLYSYTPRFDENPYSNENRTFKGFRRENG 117 IG+A + I G E + V L + L + P E E TF+G+R +G Sbjct: 72 VIGYAVRAIPRGSWIDESMVVLPEAPPLHTLPLATKVP---EPLPPLEGYTFEGYRNADG 128 Query: 118 DAGVRNELWIVPTVGCVNGIAEKMLQRFVRETGDIAP-FDNVLVLKHQYGCSQLGDDHEN 176 G +N L I +V CV G+ + +++ R+ P D V+ L H YGC + Sbjct: 129 SVGTKNLLGITTSVHCVAGVVDYVVKIIERDLLPKYPNVDGVVGLNHLYGCGVAINAPAA 188 Query: 177 TKQI--LLNAIRHPNAGG-VLVLGLGCENNELARMKEALQDVNLKRVKFLESQSVTDEME 233 I + N +PN GG V+V+GLGCE + R+ DV V+ S+ DE Sbjct: 189 VVPIRTIHNISLNPNFGGEVMVIGLGCEKLQPERLLTGTDDVQAIPVESASIVSLQDEKH 248 Query: 234 AGV-ALLKEIHEAAKGD-------KREDIPLSELKIGLKCGGSDGFSGITANPLLGRFSD 285 G +++++I + A+ +RE P SEL +G++CGGSD FSG+TANP +G SD Sbjct: 249 VGFQSMVEDILQIAERHLQKLNQRQRETCPASELVVGMQCGGSDAFSGVTANPAVGYASD 308 Query: 286 YLIAQGGSTVLTEVPEMFGAETILMQRAANEEVFHKIVDLINDFKQYFIKHDQPVYENPS 345 L+ G + + +EV E+ A +L RA NEEV ++++ + + Y NPS Sbjct: 309 LLVRCGATVMFSEVTEVRDAIHLLTPRAVNEEVGKRLLEEMEWYDNYLNMGKTDRSANPS 368 Query: 346 PGNKAGGISTLEDKSLGCTQKAGISPVTDVLKYGEVLKTKGLTLLSAPGNDLIASSALAA 405 PGNK GG++ + +K+LG K+G S + +VL G+ +GL + P +D + + A Sbjct: 369 PGNKKGGLANVVEKALGSIAKSGKSAIVEVLSPGQRPTKRGLIYAATPASDFVCGTQQVA 428 Query: 406 AGCQIVLFTTGRGTPFGTF-VPTVKVATNTELYEAKPHWIDFNAGLLAEDDVHEEYVLRE 464 +G + +FTTGRGTP+G VP +K+AT TEL +D NAG +A + E V + Sbjct: 429 SGITVQVFTTGRGTPYGLMAVPVIKMATRTELANRWFDLMDINAGTIATGEETIEEVGWK 488 Query: 465 FIHYMIEVASGQ 476 H++++VASG+ Sbjct: 489 LFHFILDVASGK 500 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: 592 Number of extensions: 35 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: 523 Length adjustment: 34 Effective length of query: 463 Effective length of database: 489 Effective search space: 226407 Effective search space used: 226407 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