Align Altronate dehydratase; EC 4.2.1.7; D-altronate hydro-lyase (uncharacterized)
to candidate HSERO_RS15800 HSERO_RS15800 D-galactarate dehydratase
Query= curated2:O34673 (497 letters) >FitnessBrowser__HerbieS:HSERO_RS15800 Length = 522 Score = 233 bits (594), Expect = 1e-65 Identities = 163/495 (32%), Positives = 257/495 (51%), Gaps = 32/495 (6%) Query: 4 FIKIHKQDNVLLALRD--IQKGERLHAYGVSIEVKDDIKRGHKIALQSIKENDSIVKYGF 61 +I ++ DNV + + D + G + + + D + +GHKIAL+ +K+ ++IV+Y Sbjct: 15 YIMMNDTDNVAIVVNDGGLPAGT---VFPDGLTLVDRVPQGHKIALRDLKQGEAIVRYDV 71 Query: 62 PIGHASQDISIGEHIHVHNTKTNLSDIQLYSYTPRFDENPYSN---ENRTFKGFRRENGD 118 IG+A +DI G I + + + P + P E TF+G+R +G Sbjct: 72 AIGYAVRDIPKGGWIE--ESLVQMPPARELDNLPIATKKPAPQPPLEGYTFEGYRNADGS 129 Query: 119 AGVRNELWIVPTVGCVNGIAEKMLQRFVRETGDIAP-FDNVLVLKHQYGCSQLGDDHENT 177 G RN L I TV CV G+ E ++R E P ++V+ L+H YGC + D N Sbjct: 130 VGTRNLLAITTTVQCVAGVVEHAVKRIRAELLPKYPNVEDVVALEHTYGCG-VAIDAPNA 188 Query: 178 K---QILLNAIRHPNAGG-VLVLGLGCENNELARM-KEALQDVN---------LKRVKFL 223 + L N +PN GG +V+ LGCE + R+ E + ++ L+ + + Sbjct: 189 GIPIRTLRNISLNPNFGGQAMVVSLGCEKLQPNRLLPENMIPIHKQGEPYVVCLQDAEHV 248 Query: 224 ESQSVTDE-MEAGVALLKEIHEAAKGDKREDIPLSELKIGLKCGGSDGFSGITANPLLGR 282 S+ D M A L E+++ +RE P S+L +G++CGGSD FSG+TANP +G Sbjct: 249 GFNSMIDSIMNMAEARLTELNKR----RRETCPASDLVVGVQCGGSDAFSGVTANPAVGF 304 Query: 283 FSDYLIAQGGSTVLTEVPEMFGAETILMQRAANEEVFHKIVDLINDFKQYFIKHDQPVYE 342 +D L+ G S + +EV E+ L RA NEEV ++ ++ + Y + Sbjct: 305 ATDLLVRAGASVMFSEVTEVRDGIDQLTSRAVNEEVAQAMIREMDWYDNYLKQGGVDRSA 364 Query: 343 NPSPGNKAGGISTLEDKSLGCTQKAGISPVTDVLKYGEVLKTKGLTLLSAPGNDLIASSA 402 N +PGNK GG++ + +K++G K+G SP++ VL G+ L+ KGL + P +D I + Sbjct: 365 NTTPGNKKGGLANIVEKAMGSIVKSGSSPISGVLSPGDKLQQKGLIYAATPASDFICGTL 424 Query: 403 LAAAGCQIVLFTTGRGTPFG-TFVPTVKVATNTELYEAKPHWIDFNAGLLAEDDVHEEYV 461 AAG + +FTTGRGTP+G VP +KVAT +L +D NAG +A + E V Sbjct: 425 QLAAGMNLHIFTTGRGTPYGLAAVPVIKVATRNDLARRWHDLMDVNAGRIASGEASIEDV 484 Query: 462 LREFIHYMIEVASGQ 476 E M++VASG+ Sbjct: 485 GWELFQLMLDVASGK 499 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: 580 Number of extensions: 28 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: 522 Length adjustment: 34 Effective length of query: 463 Effective length of database: 488 Effective search space: 225944 Effective search space used: 225944 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