Align Altronate dehydratase; D-altronate hydro-lyase; EC 4.2.1.7 (characterized)
to candidate H281DRAFT_05320 H281DRAFT_05320 galactarate dehydratase
Query= SwissProt::P42604 (495 letters) >FitnessBrowser__Burk376:H281DRAFT_05320 Length = 529 Score = 210 bits (534), Expect = 1e-58 Identities = 158/524 (30%), Positives = 259/524 (49%), Gaps = 63/524 (12%) Query: 3 YIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPI 62 YI++H DNVA+ + D G E +V + LR+ V +GHK AL D+A+G VI+Y + I Sbjct: 7 YIRVHPNDNVAIVVNDGGLG-EGAVFPDGLVLRERVPQGHKVALADLAEGDEVIRYNVVI 65 Query: 63 GYALADIAAGVHVHAHNTRTNLSDLDQYRYQPDFQDLPAQAADRE---------VQIYRR 113 GYAL + G ++ H R P +DLP + YR Sbjct: 66 GYALKALPKGSWINEHVIRMPSP--------PGLEDLPIATIKAPEMPPLEGYTFEGYRN 117 Query: 114 ANGDVGVRNELWILPTVGCVNGIAR----QIQNRFLKETNNAEGTDGVFLFSHTYGCS-- 167 A+G VG RN L I TV CV + +I++ L + N + G+ HTYGC Sbjct: 118 ADGSVGSRNILAITTTVQCVADVVEHAVVRIKSELLPKYPNVDDVVGL---GHTYGCGVA 174 Query: 168 -QLGDDHINTRTMLQNMVRHPN-AGAVLVIGLGCENNQ-----------VAAFRET---- 210 D + RT+ +N+ +PN G V+++ LGCE Q +AA + Sbjct: 175 IDAPDAMVPIRTV-RNIALNPNFGGEVMMVSLGCEKLQPERLMPPGTIPIAAAQNPSEIA 233 Query: 211 -LGDIDPERVHFMICQQQDDEIEAGIEHLHQLYNVMR----------NDKREPGKLSELK 259 +GD+ + ++ Q DE G + + + ++MR N +RE ++L Sbjct: 234 DIGDLGADENGDVVVLQ--DEAHVGFQSMVE--SIMRTAEGHLKRLNNRRRETCPAADLV 289 Query: 260 FGLECGGSDGLSGITANPMLGRFSDYVIANGGTTVLTEVPEMFGAEQLLMDHCRDEATFE 319 G++CGGSD SG+TANP +G +D ++ G T + +EV E+ L + + Sbjct: 290 VGVQCGGSDAFSGLTANPAVGFATDLLVRAGATVMFSEVTEVRDGVDQLTARAENADVAQ 349 Query: 320 KLVTMVNDFKQYFIAHDQPIYENPSPGNKAGGITTLEDKSLGCTQKAGSSVVVDVLRYGE 379 ++ + + Y N +PGNK GG++ + +K++G K+G+S + VL GE Sbjct: 350 AIIREMQWYDDYLKRGGADRSANTTPGNKKGGLSNIVEKAMGSIIKSGNSPISGVLSPGE 409 Query: 380 RLKTPGLNLLSAPGNDAVATSALAGAGCHMVLFSTGRGTPYG-GFVPTVKIATNSELAAK 438 +++ GL + P +D + + AG ++ +F+TGRGTPY VP +K+AT S+LA + Sbjct: 410 KVRQKGLIYAATPASDFICGTLQLAAGINLHVFTTGRGTPYSLAEVPVIKVATRSDLARR 469 Query: 439 KKHWIDFDAGQLIHGKA-MPQLLEEFIDTIVEFANG-KQTCNER 480 +D +AG + G A + ++ E +++ A+G K+TC E+ Sbjct: 470 WHDLMDINAGTIATGSATIEEVGWELFRFMLDVASGRKKTCAEK 513 Lambda K H 0.319 0.136 0.403 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: 649 Number of extensions: 36 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: 495 Length of database: 529 Length adjustment: 35 Effective length of query: 460 Effective length of database: 494 Effective search space: 227240 Effective search space used: 227240 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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