Align Altronate dehydratase; EC 4.2.1.7; D-altronate hydro-lyase (uncharacterized)
to candidate HSERO_RS19355 HSERO_RS19355 galactarate dehydratase
Query= curated2:O34673 (497 letters) >FitnessBrowser__HerbieS:HSERO_RS19355 Length = 511 Score = 279 bits (714), Expect = 1e-79 Identities = 166/499 (33%), Positives = 272/499 (54%), Gaps = 27/499 (5%) Query: 5 IKIHKQDNVLLALRDIQKGERLHAYGVSIEVKDDIKRGHKIALQSIKENDSIVKYGFPIG 64 I+++ D+V++A + + G L G ++V+ I GHK+A ++I + + +YG IG Sbjct: 8 IRLNPVDDVVIARQQLISGTVLQDEG-GLKVQGLIPAGHKMATRAITAGEPVKRYGQIIG 66 Query: 65 HASQDISIGEHIHVHNTKTNLSDIQLYSYTPRF--DENP--YSNENRTFKGFRRENGDAG 120 ASQDI+ G+H+H HN + +S F D P + TF G R +G Sbjct: 67 TASQDIAPGQHVHTHNLA-----MAEFSREHHFGADVKPVDFVATPATFMGIVRPDGRVA 121 Query: 121 VRNELWIVPTVGCVNGIAEKMLQRFVRET-----GDIAPFDNVLVLKHQYGCS--QLGDD 173 RN + ++ +V C A + F R+ D D V+ L H GC+ G+ Sbjct: 122 TRNYIGVLTSVNCSATAARAIADYFRRDIHPEVLADYPNIDGVVALTHGQGCALDSQGEP 181 Query: 174 HENTKQILLNAIRHPNAGGVLVLGLGCENNELARMKEALQDVNLKRVKFLESQSV----- 228 + ++ L HPN VLV+GLGCE N+++ + E+ NLK ++ + ++ Sbjct: 182 LQILRRTLAGYATHPNFAAVLVVGLGCETNQISGLMESH---NLKEGEYFHTFTIQGTGG 238 Query: 229 -TDEMEAGVALLKEIHEAAKGDKREDIPLSELKIGLKCGGSDGFSGITANPLLGRFSDYL 287 + G+ +K++ A KRE + L +GL+CGGSDG+SGITANP LG D L Sbjct: 239 TAKTVALGIEKIKKMLPKANDIKREPVSAKHLTLGLQCGGSDGYSGITANPALGAAVDLL 298 Query: 288 IAQGGSTVLTEVPEMFGAETILMQRAANEEVFHKIVDLINDFKQYFIKHDQPVYENPSPG 347 + GG+ +L+E PE++GAE +L +RA + EV K++ I +++Y K+D + NPS G Sbjct: 299 VRHGGTAILSETPEIYGAEHLLTRRAVSPEVGEKLLARIAWWEEYCAKNDAEMNNNPSAG 358 Query: 348 NKAGGISTLEDKSLGCTQKAGISPVTDVLKYGEVLKTKGLTLLSAPGNDLIASSALAAAG 407 NKAGG++T+ +KSLG K G + + DV KY E + +G + PG D I+++ A G Sbjct: 359 NKAGGLTTILEKSLGAVAKGGTTNLVDVYKYAEAVTARGFVFMDTPGYDPISATGQVAGG 418 Query: 408 CQIVLFTTGRGTPFGTF-VPTVKVATNTELYEAKPHWIDFNAGLLAEDDVHEEYVLREFI 466 ++ FTTGRG+ +G P++K+ATNT L++ + +D N G +A+ +V + + F Sbjct: 419 ANMICFTTGRGSAYGCAPAPSLKLATNTALWQRQEEDMDINCGEIADGNVTPQEIGERFF 478 Query: 467 HYMIEVASGQLVNHEKNDF 485 +++ ASG+ E + + Sbjct: 479 QMILDTASGKKTKSELHGY 497 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: 26 Number of successful extensions: 5 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: 511 Length adjustment: 34 Effective length of query: 463 Effective length of database: 477 Effective search space: 220851 Effective search space used: 220851 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