Align Altronate dehydratase; EC 4.2.1.7; D-altronate hydro-lyase (uncharacterized)
to candidate RR42_RS26650 RR42_RS26650 galactarate dehydratase
Query= curated2:O34673 (497 letters) >FitnessBrowser__Cup4G11:RR42_RS26650 Length = 507 Score = 272 bits (695), Expect = 2e-77 Identities = 160/494 (32%), Positives = 258/494 (52%), Gaps = 24/494 (4%) Query: 3 SFIKIHKQDNVLLALRDIQKGERLHAYGVSIEVKDDIKRGHKIALQSIKENDSIVKYGFP 62 + I++H DNVL+A + G+RL G + V+ + GHKIA +I + I K+ Sbjct: 5 ALIRLHANDNVLIARDALSLGQRLPELG--LRVRAQVPAGHKIAACAIAKGTQIRKFDTV 62 Query: 63 IGHASQDISIGEHIHVHNTKTN--------LSDIQLYSYTPRFDENPYSNENRTFKGFRR 114 IG A +DI G+H+H HN D++ Y P E TF GF R Sbjct: 63 IGVAERDIEAGDHVHSHNLALVDFYRDPGFCQDVRPVDYVPEA-------ERATFMGFVR 115 Query: 115 ENGDAGVRNELWIVPTVGCVNGIAEKMLQRFVRETGDIAP-FDNVLVLKHQYGC--SQLG 171 +G G RN + I+ +V C + + F E P D V GC S Sbjct: 116 PDGRVGTRNFIGILSSVNCSATVIRHIADHFTPERMAAYPNVDGVAAFAQSSGCGMSSPS 175 Query: 172 DDHENTKQILLNAIRHPNAGGVLVLGLGCENNELARMKEA---LQDVNLKRVKFLESQSV 228 + + ++ L RHPN GVL++GLGCE N++A + E+ + +++ + +S Sbjct: 176 EHFDVLRRTLAGYARHPNLAGVLIVGLGCERNQVAGLMESQGLVPGSHVRTMVMQDSGGT 235 Query: 229 TDEMEAGVALLKEIHEAAKGDKREDIPLSELKIGLKCGGSDGFSGITANPLLGRFSDYLI 288 ++AG+ ++ + A R+ +P S LKIGL+CGGSDGFSGI+ANP LG D L+ Sbjct: 236 AATIQAGIRAIEAMLPGANTATRQPVPASHLKIGLECGGSDGFSGISANPALGAAMDILV 295 Query: 289 AQGGSTVLTEVPEMFGAETILMQRAANEEVFHKIVDLINDFKQYFIKHDQPVYENPSPGN 348 GG+ +L+E PE+ G E +L +RA EV K++D + +++Y + GN Sbjct: 296 RHGGTAILSETPEIHGVEYMLTRRAVTPEVGQKLLDRLAWWERYTAGQNAQFNGVVGHGN 355 Query: 349 KAGGISTLEDKSLGCTQKAGISPVTDVLKYGEVLKTKGLTLLSAPGNDLIASSALAAAGC 408 + GG++ + +KSLG K G +P+ V +Y E ++ G + +PG D +A++ A+G Sbjct: 356 QQGGLANIFEKSLGSAMKGGTTPLQAVYEYAEPIEQSGFVFMDSPGYDPVAATGQIASGA 415 Query: 409 QIVLFTTGRGTPFGTF-VPTVKVATNTELYEAKPHWIDFNAGLLAEDDVHEEYVLREFIH 467 ++ FTTGRG+ FG+ PT+K+A+NT +Y +D N GL+ + ++ + + + Sbjct: 416 NLICFTTGRGSMFGSKPAPTIKLASNTPMYTRLEGDMDINCGLVLDGELTVDEMGQRIFE 475 Query: 468 YMIEVASGQLVNHE 481 +++E ASG E Sbjct: 476 HILEAASGHPTKSE 489 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: 569 Number of extensions: 25 Number of successful extensions: 8 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: 507 Length adjustment: 34 Effective length of query: 463 Effective length of database: 473 Effective search space: 218999 Effective search space used: 218999 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