Align Altronate dehydratase; EC 4.2.1.7; D-altronate hydro-lyase (uncharacterized)
to candidate H281DRAFT_00666 H281DRAFT_00666 altronate hydrolase
Query= curated2:O34673 (497 letters) >FitnessBrowser__Burk376:H281DRAFT_00666 Length = 518 Score = 281 bits (719), Expect = 4e-80 Identities = 167/496 (33%), Positives = 268/496 (54%), Gaps = 22/496 (4%) Query: 5 IKIHKQDNVLLALRDIQKGERLHAYGVSIEVKDDIKRGHKIALQSIKENDSIVKYGFPIG 64 I++H D+V++A R + G R+ + + + I GHKIA ++I + + +Y IG Sbjct: 16 IRLHANDDVVIATRQLMSGARIASE--DLVIAGLIPPGHKIATRAIAAGEPVKRYNQIIG 73 Query: 65 HASQDISIGEHIHVHNTKTNLSDI-QLYSYTPRFDENPYSNENRTFKGFRRENGDAGVRN 123 A+Q I G+H+HV N +++ + + + Y+ E TF G RR +G RN Sbjct: 74 VATQPIQRGQHVHVQNL--GMAEFSRAHEFGVAVHATQYAAEPATFMGIRRADGRVATRN 131 Query: 124 ELWIVPTVGCVNGIAEKMLQRFVRETG-----DIAPFDNVLVLKHQYGCS--QLGDDHEN 176 + ++ +V C +A + F R+ D D V+ L H GC LG+ Sbjct: 132 YIGVLTSVNCSATVARAIADHFRRDVNPHALADYPNVDGVVALTHGLGCGIDTLGEGLAV 191 Query: 177 TKQILLNAIRHPNAGGVLVLGLGCENNELARMKEALQDVNLKRVKFLESQSVTDE----- 231 ++ L HPN VL +GLGCE N++A + L+ LK + L S ++ D Sbjct: 192 LRRTLAGYAVHPNFHSVLFVGLGCETNQIAGV---LESAGLKDTEQLRSFTIQDSGGSKK 248 Query: 232 -MEAGVALLKEIHEAAKGDKREDIPLSELKIGLKCGGSDGFSGITANPLLGRFSDYLIAQ 290 +E G+A++ E+ A KRE +P S L +GL+CGGSDG+SGI+ANP LG D L+ Sbjct: 249 TIERGIAMVNEMLADANRVKREPLPASHLIVGLQCGGSDGYSGISANPALGAAVDLLVQH 308 Query: 291 GGSTVLTEVPEMFGAETILMQRAANEEVFHKIVDLINDFKQYFIKHDQPVYENPSPGNKA 350 GG+ +L+E PE++GAE +L +RA + V K++ I +++Y ++ + NPS GNK Sbjct: 309 GGTAILSETPEVYGAEHLLTRRAVSRAVGEKLLARIAWWEEYCARNGAALDNNPSAGNKV 368 Query: 351 GGISTLEDKSLGCTQKAGISPVTDVLKYGEVLKTKGLTLLSAPGNDLIASSALAAAGCQI 410 GG++T+ +KSLG K G + + DV +Y E + KG + +PG D ++++ AAG + Sbjct: 369 GGLTTILEKSLGAVAKGGTTNLVDVYQYAERIDAKGFVFMDSPGYDPVSATGQVAAGANL 428 Query: 411 VLFTTGRGTPFGTF-VPTVKVATNTELYEAKPHWIDFNAGLLAEDDVHEEYVLREFIHYM 469 + FTTGRG+ +G P++K+ATNT L+E + +D N G + + E + M Sbjct: 429 ICFTTGRGSAYGCAPSPSLKLATNTALWERQEDDMDINCGGVIDGSASIEELGEAIFAQM 488 Query: 470 IEVASGQLVNHEKNDF 485 +E ASG E N + Sbjct: 489 LECASGVPSKSEVNGY 504 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: 581 Number of extensions: 38 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: 518 Length adjustment: 34 Effective length of query: 463 Effective length of database: 484 Effective search space: 224092 Effective search space used: 224092 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