Align D-mannonate oxidoreductase; EC 1.1.1.57; Fructuronate reductase (uncharacterized)
to candidate Pf1N1B4_4846 Multiple polyol-specific dehydrogenase (EC 1.1.1.-)
Query= curated2:P39160 (486 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4846 Length = 491 Score = 343 bits (881), Expect = 6e-99 Identities = 189/470 (40%), Positives = 271/470 (57%), Gaps = 6/470 (1%) Query: 11 VARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDS-DWGICEVNLMPGNDRVLI 69 VA P++ S I H+G G FHRAHQA YT L+ + ++ DW IC V L DR Sbjct: 15 VALPAYTLSDTRQGIAHIGVGGFHRAHQAYYTDALMNTGEALDWAICGVGLR-AEDRRAR 73 Query: 70 ENLKKQQLLYTVAEKG-AESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVT 128 ++LK+Q L+T+ E G A+ E+++IG++++ L E D E +++ +A P IVSLT+T Sbjct: 74 DDLKEQDYLFTLFELGDADDAEVRVIGAIRDMLLAE-DSPEVLIDKLADPDIRIVSLTIT 132 Query: 129 EKGYCADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNV 188 E GYC D ++G+ + P I+HDL +P APK+ G++ AL RR G AFT+MSCDN+ Sbjct: 133 EGGYCIDDSNGEFMAHLPQIQHDLAHPNAPKTVFGFLCAALAKRRAAGTPAFTLMSCDNL 192 Query: 189 RENGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYD 248 NG V + A+L A RD L WIE +V+FP MVDRI P + E ++ D+ + D Sbjct: 193 PHNGAVTRKALLAFAALRDADLRDWIERHVSFPNAMVDRITPMTSTEHRLQLHDKHSIDD 252 Query: 249 PCAIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYL 308 + CEPF QWV+ED FVNGRP W+KVG QF DV P+E MK+++LNGSH L YLG+L Sbjct: 253 AWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIKLLNGSHLALTYLGFL 312 Query: 309 GGYETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTW 368 GY + +T+ +P + + A M + P L+ G DL Y L+ RFSN ++ + Sbjct: 313 KGYRFVHETMNDPLFVRYMRAYMDLDVTPQLAPVPGIDLTEYKNTLVARFSNQAIADQLE 372 Query: 369 QIAMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLA 428 ++ DGS K P+ + + + +G + AL VA W Y +GVDE G + DP A Sbjct: 373 RVCSDGSSKFPKFTVPTINCLIADGQETKRAALVVAAWALYLKGVDENGQTYAIPDPRAA 432 Query: 429 EFQKINAQYQGADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERG 478 Q + A + LL + IF +P++ +FV A L E G Sbjct: 433 FCQALVA--DDVLITQRLLEVEEIFGTAIPRSPEFVAAFEWCCNSLREVG 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: 641 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: 491 Length adjustment: 34 Effective length of query: 452 Effective length of database: 457 Effective search space: 206564 Effective search space used: 206564 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