Align D-mannonate oxidoreductase; EC 1.1.1.57; Fructuronate reductase (uncharacterized)
to candidate AO356_27690 AO356_27690 mannitol dehydrogenase
Query= curated2:P39160 (486 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27690 Length = 493 Score = 355 bits (911), Expect = e-102 Identities = 192/473 (40%), Positives = 275/473 (58%), Gaps = 6/473 (1%) Query: 8 NLPVARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLES-TDSDWGICEVNLMPGNDR 66 N VA P++ + I H+G G FHRAHQA YT L+ + D DW IC V L DR Sbjct: 12 NPDVALPAYPLGDIRQGIAHIGVGGFHRAHQAYYTDALMNTGVDLDWAICGVGLR-AEDR 70 Query: 67 VLIENLKKQQLLYTVAEKG-AESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSL 125 ++L Q L+T+ E G + TE+++IG++ + L E DG + +++ +A PQ IVSL Sbjct: 71 RARDDLASQDYLFTLYELGDTDDTEVRVIGAINDMLLAE-DGAQALIDKLADPQIRIVSL 129 Query: 126 TVTEKGYCADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSC 185 T+TE GYC D ++G+ + P I+HDL +P APK+ G++ AL RR G+ AFT+MSC Sbjct: 130 TITEGGYCIDDSNGEFMAHLPQIQHDLNHPEAPKTVFGFLCAALAKRRAAGIPAFTLMSC 189 Query: 186 DNVRENGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLG 245 DN+ NG V + A+L A RD +L WI+ NV+FP MVDRI P + ++ D+ G Sbjct: 190 DNLPHNGAVTRKALLAFAALRDAELGQWIDRNVSFPNAMVDRITPMTSVTHRLQLHDEHG 249 Query: 246 VYDPCAIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYL 305 + D + CEPF QWV+ED FV+GRP W+KVG QF DV P+E MK+++LNGSH L YL Sbjct: 250 IDDAWPVVCEPFVQWVLEDKFVSGRPAWEKVGVQFTDDVSPYEEMKIKLLNGSHLALTYL 309 Query: 306 GYLGGYETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRH 365 G+L GY + +T+ +P + + A M + P L+ G DL Y L+ERFSN ++ Sbjct: 310 GFLKGYRFVHETMNDPLFVRYIRAYMDLDVTPQLAPVPGIDLTDYKNTLVERFSNQAIAD 369 Query: 366 RTWQIAMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDP 425 + ++ DGS K P+ + + + +GG R AL VA W Y +GVDE G + DP Sbjct: 370 QLERVCSDGSSKFPKFTVPTINRLIADGGETRRAALVVAAWAVYLKGVDENGVTYSIPDP 429 Query: 426 MLAEFQKINAQYQGADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERG 478 A Q + A A + +L + IF +P++ +FV A L E G Sbjct: 430 RAAFCQALVA--DDALVTQRMLEVEEIFGTAIPRSPEFVAAFEWCCNSLREHG 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: 646 Number of extensions: 32 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: 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