Align D-mannonate oxidoreductase; EC 1.1.1.57; Fructuronate reductase (uncharacterized)
to candidate GFF1300 PGA1_c13160 mannitol 2-dehydrogenase MtlK
Query= curated2:P39160 (486 letters) >FitnessBrowser__Phaeo:GFF1300 Length = 488 Score = 280 bits (716), Expect = 8e-80 Identities = 172/423 (40%), Positives = 234/423 (55%), Gaps = 8/423 (1%) Query: 7 SNLP--VARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLES-TDSDWGICEVNLMPG 63 S LP + RPS+D + + IVH+G G FHRAHQA Y H L++S DWGI + Sbjct: 9 SQLPQTIGRPSYDRAEISPGIVHIGLGNFHRAHQAWYLHALMQSGLAMDWGIIGAGVRAA 68 Query: 64 NDRVLIENLKKQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIV 123 D + + L Q L T+ E ++IG + + L E D ++ MA IV Sbjct: 69 -DAGMRDRLLAQDCLTTLIELDPTGRSAEVIGPLIDFLPVEADNAS-LIRCMAGSPIRIV 126 Query: 124 SLTVTEKGYCADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVM 183 SLTVTE GY DA LDLN+ I+HD+ P P++ G IVEALRLRR +GL AFTV Sbjct: 127 SLTVTEGGYYQDAQHKGLDLNHEDIRHDIARPDRPRTVFGAIVEALRLRRGRGLPAFTVQ 186 Query: 184 SCDNVRENGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQ 243 SCDN++ NG + + AV+ LAQ DP+LAAWI++ FP +MVD IVPA P + +A Sbjct: 187 SCDNLQGNGQITRTAVVTLAQQTDPELAAWIDQTGAFPNSMVDCIVPATGPAEI-ALARG 245 Query: 244 LGVYDPCAIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLA 303 G+ D + E +R WVIED F GRP WD GA F DV +E MK+R+LN H LA Sbjct: 246 YGIEDTAPVTHENYRHWVIEDEFCAGRPPWDLAGAIFTDDVHGYESMKIRVLNAGHQVLA 305 Query: 304 YLGYLGGYETIADTVTNPAYRKAAFALMMQEQAP-TLSMPEGTDLNAYATLLIERFSNPS 362 G L TIAD + +P + E P +++PE + Y TL+ RFSNP Sbjct: 306 NAGELLSIATIADCMKDPLLAAFFRTVQTAEILPHVIAVPEMAPKD-YLTLIEARFSNPE 364 Query: 363 LRHRTWQIAMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDV 422 +R T ++A DGS + P ++ +R +++ G+ L L A W + G+ E + I Sbjct: 365 IRDTTRRVAYDGSSRHPGFVMPILRDAVRSKGAIDGLCLVEALWAQMCTGLREDASEIAP 424 Query: 423 VDP 425 DP Sbjct: 425 NDP 427 Lambda K H 0.320 0.135 0.408 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: 603 Number of extensions: 20 Number of successful extensions: 4 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: 486 Length of database: 488 Length adjustment: 34 Effective length of query: 452 Effective length of database: 454 Effective search space: 205208 Effective search space used: 205208 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 (21.8 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