Align D-mannonate oxidoreductase; EC 1.1.1.57; Fructuronate reductase (uncharacterized)
to candidate GFF2489 PS417_12695 mannitol dehydrogenase
Query= curated2:P39160 (486 letters) >FitnessBrowser__WCS417:GFF2489 Length = 493 Score = 334 bits (856), Expect = 5e-96 Identities = 187/472 (39%), Positives = 266/472 (56%), Gaps = 6/472 (1%) Query: 9 LPVARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLES-TDSDWGICEVNLMPGNDRV 67 L V P+++ + I H+G G FHRAHQA YT L+ + DW IC V L DR Sbjct: 13 LQVKLPTYEIASTTQGIAHIGVGGFHRAHQAYYTDALMNTGVGLDWSICGVGLR-AEDRK 71 Query: 68 LIENLKKQQLLYTVAEKG-AESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLT 126 ++L Q L+T+ E G + TE+++IGS+ + L E DG + +++ +A P IVSLT Sbjct: 72 ARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAE-DGAQALIDKLADPAIRIVSLT 130 Query: 127 VTEKGYCADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCD 186 +TE GYC D ++G+ + P I+HDL +P+APK+ G+I AL RR G AFTVMSCD Sbjct: 131 ITEGGYCIDDSNGEFMAHLPQIQHDLAHPSAPKTVFGFICAALTKRRAAGTPAFTVMSCD 190 Query: 187 NVRENGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGV 246 N+ NG V + A+L A + +L WI+ NV+FP MVDRI P + ++ D G+ Sbjct: 191 NLPHNGAVTRKALLAFAALHNAELHDWIKANVSFPNAMVDRITPMTSTAHRLQLHDDHGI 250 Query: 247 YDPCAIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLG 306 D + CEPF QWV+ED FVNGRP W+ VG QF DV P+E MK+ +LNGSH L YLG Sbjct: 251 DDAWPVVCEPFVQWVLEDKFVNGRPAWETVGVQFTDDVTPYEEMKIGLLNGSHLALTYLG 310 Query: 307 YLGGYETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHR 366 +L GY + +T+ +P + A M + P L+ G DL Y L++RFSN ++ + Sbjct: 311 FLKGYRFVHETMNDPVFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIADQ 370 Query: 367 TWQIAMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPM 426 ++ DGS K P+ + + + +G AL VA W Y +GVDE G + + DP Sbjct: 371 LERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENGVSYKIPDPR 430 Query: 427 LAEFQKINAQYQGADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERG 478 AEF + A + LL + IF +P + FV A + L + G Sbjct: 431 -AEFCQ-GLVSDDALISQRLLAVEEIFGTAIPNSPGFVAAFERCFVSLRDNG 480 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: 651 Number of extensions: 38 Number of successful extensions: 2 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: 493 Length adjustment: 34 Effective length of query: 452 Effective length of database: 459 Effective search space: 207468 Effective search space used: 207468 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