Align Altronate dehydratase; D-altronate hydro-lyase; EC 4.2.1.7 (characterized)
to candidate RR42_RS34975 RR42_RS34975 galactarate dehydratase
Query= SwissProt::P42604 (495 letters) >FitnessBrowser__Cup4G11:RR42_RS34975 Length = 515 Score = 256 bits (653), Expect = 2e-72 Identities = 165/495 (33%), Positives = 252/495 (50%), Gaps = 18/495 (3%) Query: 4 IKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIG 63 I+IH D++ +A L GT ++ + V++ V GHK A+ IA GA V +Y IG Sbjct: 10 IRIHPADDIVIACRQLVPGTVIAAEG--VSVASLVPPGHKLAVRAIAAGAPVRRYNQIIG 67 Query: 64 YALADIAAGVHVHAHNTRTNLSDLDQYRYQPDFQDLPAQAADREVQIYRRANGDVGVRNE 123 +A IA G HVH HN +Y D + A +RA+G V RN Sbjct: 68 FARQPIAPGQHVHTHNLAMG-EFTREYAAGADARATEYVDAPASFDGIKRADGSVATRNY 126 Query: 124 LWILPTVGCVNGIARQIQNRFLKETNNAE-----GTDGVFLFSHTYGCS--QLGDDHINT 176 + IL +V C +AR I + F +E DGV +H GC+ G++ Sbjct: 127 IGILTSVNCSATVARAIADHFRRELRPEALAAFPNVDGVVALTHGAGCATDSEGENLRVL 186 Query: 177 RTMLQNMVRHPNAGAVLVIGLGCENNQV---AAFRETLGDIDPERVHFMICQQQDDEIEA 233 R L RHPN AVLV+GLGCE NQ+ A + G R+H Q A Sbjct: 187 RRTLAGYARHPNFAAVLVVGLGCEANQIDGLLAEGDLAGMAGGPRLHAFNIQDSGGTAGA 246 Query: 234 ---GIEHLHQLYNVMRNDKREPGKLSELKFGLECGGSDGLSGITANPMLGRFSDYVIANG 290 G+ + L R+ S + GL+CGGSDG SG+TANP LG D ++ +G Sbjct: 247 VARGVAIVQDLLADANRVSRQAVPASHITVGLQCGGSDGYSGLTANPALGAAVDLLVRHG 306 Query: 291 GTTVLTEVPEMFGAEQLLMDHCRDEATFEKLVTMVNDFKQYFIAHDQPIYENPSPGNKAG 350 G +L+E PE++GAE LL A +L+ + ++ Y + + NPS GNKAG Sbjct: 307 GGAILSETPEIYGAEHLLTRRAASPAVAARLLERIRWWEDYCARNHGSMDNNPSAGNKAG 366 Query: 351 GITTLEDKSLGCTQKAGSSVVVDVLRYGERLKTPGLNLLSAPGNDAVATSALAGAGCHMV 410 G+TT+ +KSLG K+G++ +V+V + + ++ GL + PG D V+ + G +++ Sbjct: 367 GLTTILEKSLGAVAKSGTTNLVEVYEFAQPVRARGLVFMDTPGYDPVSATGQVAGGANLI 426 Query: 411 LFSTGRGTPYG-GFVPTVKIATNSELAAKKKHWIDFDAGQLIHGKA-MPQLLEEFIDTIV 468 F+TGRG+ YG P++K+ATNS L ++ ID + G ++ G A + E+ ++ Sbjct: 427 CFTTGRGSAYGCAPSPSLKLATNSALWQRQADDIDINCGDIVDGGASIAHKGEQIFRRML 486 Query: 469 EFANGKQTCNERNDF 483 E A+G++T +E + + Sbjct: 487 ETASGRKTKSELHGY 501 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: 688 Number of extensions: 39 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: 495 Length of database: 515 Length adjustment: 34 Effective length of query: 461 Effective length of database: 481 Effective search space: 221741 Effective search space used: 221741 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