Align Altronate dehydratase; EC 4.2.1.7; D-altronate hydro-lyase (uncharacterized)
to candidate BPHYT_RS27220 BPHYT_RS27220 galactarate dehydratase
Query= curated2:O34673 (497 letters) >FitnessBrowser__BFirm:BPHYT_RS27220 Length = 508 Score = 305 bits (780), Expect = 3e-87 Identities = 168/489 (34%), Positives = 274/489 (56%), Gaps = 7/489 (1%) Query: 2 KSFIKIHKQDNVLLALRDIQKGERLHAYGVSIEVKDDIKRGHKIALQSIKENDSIVKYGF 61 ++ + +H +DNV +ALR ++ G + A G + V+ I GHK+A++ I ++ KY Sbjct: 4 QTIVILHNEDNVAVALRALEAGTPVEAGGQRVVVRGSIAAGHKLAIRRIARGSAVTKYRQ 63 Query: 62 PIGHASQDISIGEHIHVHNTKTNLSDIQLYSYTPRFDENPYSNENRTFKGFRRENGDAGV 121 IG A D+ GEH+HVHN +++ + F+GF R +G G Sbjct: 64 TIGIALADVEPGEHVHVHNVGMPEHHPHRPTHSDAVRSLAPVDRPGAFQGFVRADGQVGT 123 Query: 122 RNELWIVPTVGCVNGIAEKMLQRFVRETGD-IAPFDNVLVLKHQYGC--SQLGDDHENTK 178 RN + ++ +V C + + F + D + D V+ + HQ GC S GD + Sbjct: 124 RNYIGVIASVNCSASVCHAIADAFKGDAMDPFSTVDGVVAITHQSGCGMSATGDGMALLR 183 Query: 179 QILLNAIRHPNAGGVLVLGLGCENNELARMKEALQDVNLKRVKFLESQS---VTDEMEAG 235 + L +PN GVL++GLGCE N+++ + +L+ + V+ L Q V + + G Sbjct: 184 RTLTGYACNPNFAGVLLVGLGCEVNQVSGLTRSLEAGSPALVETLVIQDEGGVRETVARG 243 Query: 236 VALLKEIHEAAKGDKREDIPLSELKIGLKCGGSDGFSGITANPLLGRFSDYLIAQGGSTV 295 +A+++E+ AA +R ++P + LK+GL+CGGSDG+SGITANP LG D L+ GG+ + Sbjct: 244 IAIVREMLSAASRIRRIEVPAARLKVGLQCGGSDGYSGITANPALGAAVDLLVRHGGTAI 303 Query: 296 LTEVPEMFGAETILMQRAANEEVFHKIVDLINDFKQYFIKHDQPVYENPSPGNKAGGIST 355 L+E PE++GAE +L RA + +V +++D + +++Y + + NPSPGNKAGGI+T Sbjct: 304 LSETPEIYGAEHLLTARAVSSDVAGRLLDKLRWWERYAAEAGGDMNNNPSPGNKAGGITT 363 Query: 356 LEDKSLGCTQKAGISPVTDVLKYGEVLKTKGLTLLSAPGNDLIASSALAAAGCQIVLFTT 415 + +KSLG K G + + V +Y E GL + PG D ++++ A G +V FTT Sbjct: 364 ILEKSLGAVSKGGSTALNAVYEYAERASESGLVFMDTPGYDPVSATGQIAGGANLVCFTT 423 Query: 416 GRGTPFGTF-VPTVKVATNTELYEAKPHWIDFNAGLLAEDDVHEEYVLREFIHYMIEVAS 474 GRG+ FG+ VPT+K+AT T L+E +DFN G + + + E + M+++AS Sbjct: 424 GRGSVFGSKPVPTIKLATTTGLFERMRADMDFNCGQIVDGSLTVEQAGAQVFQLMLDIAS 483 Query: 475 GQLVNHEKN 483 G + E+N Sbjct: 484 GTKTHSEQN 492 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: 594 Number of extensions: 19 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: 508 Length adjustment: 34 Effective length of query: 463 Effective length of database: 474 Effective search space: 219462 Effective search space used: 219462 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